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cleartomark
%%EndFont
%%BeginFont: CMR6
%!PS-AdobeFont-1.1: CMR6 1.0
%%CreationDate: 1991 Aug 20 16:39:02
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.0) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMR6) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle 0 def
/isFixedPitch false def
end readonly def
/FontName /CMR6 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 0 /Gamma put
dup 40 /parenleft put
dup 41 /parenright put
dup 49 /one put
dup 61 /equal put
readonly def
/FontBBox{-20 -250 1193 750}readonly def
/UniqueXX 5000789 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMMI6
%!PS-AdobeFont-1.1: CMMI6 1.100
%%CreationDate: 1996 Jul 23 07:53:52
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.100) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMMI6) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle -14.04 def
/isFixedPitch false def
end readonly def
/FontName /CMMI6 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 11 /alpha put
dup 75 /K put
dup 107 /k put
dup 108 /l put
readonly def
/FontBBox{11 -250 1241 750}readonly def
/UniqueXX 5087381 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMR9
%!PS-AdobeFont-1.1: CMR9 1.0
%%CreationDate: 1991 Aug 20 16:39:59
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.0) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMR9) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle 0 def
/isFixedPitch false def
end readonly def
/FontName /CMR9 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 40 /parenleft put
dup 41 /parenright put
dup 48 /zero put
dup 50 /two put
dup 61 /equal put
dup 108 /l put
dup 110 /n put
readonly def
/FontBBox{-39 -250 1036 750}readonly def
/UniqueXX 5000792 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMSY9
%!PS-AdobeFont-1.1: CMSY9 1.0
%%CreationDate: 1991 Aug 15 07:22:27
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.0) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMSY9) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle -14.035 def
/isFixedPitch false def
end readonly def
/FontName /CMSY9 def
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/FontMatrix [0.001 0 0 0.001 0 0] readonly def
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dup 104 /angbracketleft put
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dup 106 /bar put
readonly def
/FontBBox{-30 -958 1146 777}readonly def
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currentdict end
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cleartomark
%%EndFont
%%BeginFont: CMMI5
%!PS-AdobeFont-1.1: CMMI5 1.100
%%CreationDate: 1996 Aug 02 08:21:10
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.100) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMMI5) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle -14.04 def
/isFixedPitch false def
end readonly def
/FontName /CMMI5 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
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dup 75 /K put
dup 105 /i put
dup 106 /j put
dup 107 /k put
dup 108 /l put
dup 109 /m put
dup 110 /n put
dup 116 /t put
readonly def
/FontBBox{37 -250 1349 750}readonly def
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currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: MSAM10
%!PS-AdobeFont-1.1: MSAM10 2.1
%%CreationDate: 1993 Sep 17 09:05:00
% Math Symbol fonts were designed by the American Mathematical Society.
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (2.1) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (MSAM10) readonly def
/FamilyName (Euler) readonly def
/Weight (Medium) readonly def
/ItalicAngle 0 def
/isFixedPitch false def
end readonly def
/FontName /MSAM10 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 44 /defines put
readonly def
/FontBBox{8 -463 1331 1003}readonly def
/UniqueXX 5031981 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMMI9
%!PS-AdobeFont-1.1: CMMI9 1.100
%%CreationDate: 1996 Jul 23 07:53:55
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.100) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMMI9) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle -14.04 def
/isFixedPitch false def
end readonly def
/FontName /CMMI9 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 11 /alpha put
dup 18 /theta put
dup 30 /phi put
dup 58 /period put
dup 59 /comma put
dup 62 /greater put
dup 67 /C put
dup 72 /H put
dup 77 /M put
dup 107 /k put
dup 108 /l put
dup 110 /n put
dup 120 /x put
dup 121 /y put
dup 126 /vector put
readonly def
/FontBBox{-29 -250 1075 750}readonly def
/UniqueXX 5087384 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMBX9
%!PS-AdobeFont-1.1: CMBX9 1.0
%%CreationDate: 1991 Aug 20 16:36:25
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.0) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMBX9) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Bold) readonly def
/ItalicAngle 0 def
/isFixedPitch false def
end readonly def
/FontName /CMBX9 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 65 /A put
readonly def
/FontBBox{-58 -250 1195 750}readonly def
/UniqueXX 5000767 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMBX10
%!PS-AdobeFont-1.1: CMBX10 1.00B
%%CreationDate: 1992 Feb 19 19:54:06
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.00B) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMBX10) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Bold) readonly def
/ItalicAngle 0 def
/isFixedPitch false def
end readonly def
/FontName /CMBX10 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 65 /A put
readonly def
/FontBBox{-301 -250 1164 946}readonly def
/UniqueXX 5000768 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMSY10
%!PS-AdobeFont-1.1: CMSY10 1.0
%%CreationDate: 1991 Aug 15 07:20:57
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.0) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMSY10) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle -14.035 def
/isFixedPitch false def
end readonly def
/FontName /CMSY10 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 0 /minus put
dup 1 /periodcentered put
dup 6 /plusminus put
dup 20 /lessequal put
dup 24 /similar put
dup 47 /proportional put
dup 50 /element put
dup 70 /F put
dup 77 /M put
dup 102 /braceleft put
dup 103 /braceright put
dup 104 /angbracketleft put
dup 105 /angbracketright put
dup 106 /bar put
dup 120 /section put
readonly def
/FontBBox{-29 -960 1116 775}readonly def
/UniqueXX 5000820 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMR10
%!PS-AdobeFont-1.1: CMR10 1.00B
%%CreationDate: 1992 Feb 19 19:54:52
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.00B) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMR10) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle 0 def
/isFixedPitch false def
end readonly def
/FontName /CMR10 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 2 /Theta put
dup 9 /Psi put
dup 22 /macron put
dup 40 /parenleft put
dup 41 /parenright put
dup 43 /plus put
dup 48 /zero put
dup 49 /one put
dup 50 /two put
dup 51 /three put
dup 52 /four put
dup 61 /equal put
dup 91 /bracketleft put
dup 93 /bracketright put
dup 101 /e put
dup 108 /l put
dup 110 /n put
dup 112 /p put
dup 120 /x put
readonly def
/FontBBox{-251 -250 1009 969}readonly def
/UniqueXX 5000793 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMR7
%!PS-AdobeFont-1.1: CMR7 1.0
%%CreationDate: 1991 Aug 20 16:39:21
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.0) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMR7) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle 0 def
/isFixedPitch false def
end readonly def
/FontName /CMR7 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 0 /Gamma put
dup 40 /parenleft put
dup 41 /parenright put
dup 43 /plus put
dup 48 /zero put
dup 49 /one put
dup 50 /two put
dup 52 /four put
dup 58 /colon put
dup 61 /equal put
dup 103 /g put
dup 108 /l put
dup 111 /o put
readonly def
/FontBBox{-27 -250 1122 750}readonly def
/UniqueXX 5000790 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMMI7
%!PS-AdobeFont-1.1: CMMI7 1.100
%%CreationDate: 1996 Jul 23 07:53:53
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.100) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMMI7) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle -14.04 def
/isFixedPitch false def
end readonly def
/FontName /CMMI7 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 14 /delta put
dup 18 /theta put
dup 59 /comma put
dup 64 /partialdiff put
dup 73 /I put
dup 76 /L put
dup 77 /M put
dup 78 /N put
dup 84 /T put
dup 98 /b put
dup 103 /g put
dup 104 /h put
dup 105 /i put
dup 106 /j put
dup 107 /k put
dup 108 /l put
dup 109 /m put
dup 110 /n put
dup 113 /q put
dup 116 /t put
dup 120 /x put
dup 121 /y put
readonly def
/FontBBox{0 -250 1171 750}readonly def
/UniqueXX 5087382 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMMI10
%!PS-AdobeFont-1.1: CMMI10 1.100
%%CreationDate: 1996 Jul 23 07:53:57
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.100) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMMI10) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle -14.04 def
/isFixedPitch false def
end readonly def
/FontName /CMMI10 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 11 /alpha put
dup 14 /delta put
dup 18 /theta put
dup 25 /pi put
dup 30 /phi put
dup 58 /period put
dup 59 /comma put
dup 61 /slash put
dup 65 /A put
dup 66 /B put
dup 73 /I put
dup 76 /L put
dup 77 /M put
dup 81 /Q put
dup 84 /T put
dup 85 /U put
dup 88 /X put
dup 89 /Y put
dup 97 /a put
dup 98 /b put
dup 100 /d put
dup 101 /e put
dup 104 /h put
dup 105 /i put
dup 106 /j put
dup 107 /k put
dup 108 /l put
dup 112 /p put
dup 113 /q put
dup 116 /t put
dup 120 /x put
dup 121 /y put
dup 126 /vector put
readonly def
/FontBBox{-32 -250 1048 750}readonly def
/UniqueXX 5087385 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMSY5
%!PS-AdobeFont-1.1: CMSY5 1.0
%%CreationDate: 1991 Aug 15 07:21:16
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.0) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMSY5) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle -14.035 def
/isFixedPitch false def
end readonly def
/FontName /CMSY5 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 0 /minus put
dup 48 /prime put
readonly def
/FontBBox{21 -944 1448 791}readonly def
/UniqueXX 5000815 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMR5
%!PS-AdobeFont-1.1: CMR5 1.00B
%%CreationDate: 1992 Feb 19 19:55:02
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.00B) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMR5) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle 0 def
/isFixedPitch false def
end readonly def
/FontName /CMR5 def
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/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
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0 1 255 {1 index exch /.notdef put} for
dup 40 /parenleft put
dup 41 /parenright put
dup 43 /plus put
dup 48 /zero put
dup 49 /one put
dup 61 /equal put
readonly def
/FontBBox{-341 -250 1304 965}readonly def
/UniqueXX 5000788 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMSY6
%!PS-AdobeFont-1.1: CMSY6 1.0
%%CreationDate: 1991 Aug 15 07:21:34
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.0) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMSY6) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle -14.035 def
/isFixedPitch false def
end readonly def
/FontName /CMSY6 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 0 /minus put
dup 3 /asteriskmath put
readonly def
/FontBBox{-4 -948 1329 786}readonly def
/UniqueXX 5000816 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
%%BeginFont: CMSY7
%!PS-AdobeFont-1.1: CMSY7 1.0
%%CreationDate: 1991 Aug 15 07:21:52
% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
11 dict begin
/FontInfo 7 dict dup begin
/version (1.0) readonly def
/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
/FullName (CMSY7) readonly def
/FamilyName (Computer Modern) readonly def
/Weight (Medium) readonly def
/ItalicAngle -14.035 def
/isFixedPitch false def
end readonly def
/FontName /CMSY7 def
/PaintType 0 def
/FontType 1 def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 0 /minus put
dup 2 /multiply put
dup 3 /asteriskmath put
dup 48 /prime put
readonly def
/FontBBox{-15 -951 1252 782}readonly def
/UniqueXX 5000817 def
currentdict end
currentfile eexec
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cleartomark
%%EndFont
TeXDict begin 40258431 52099146 1000 600 600 (GenomeSci_final_short.dvi)
@start /Fa 198[29 29 29 29 29 2[29 29 29 1[15 46[{
TeXBase1Encoding ReEncodeFont}9 58.1154 /Times-Bold rf
/Fb 174[54 60 80[{}2 49.8132 /CMEX10 rf /Fc 194[47 11[30
7[24 24 39[38{}5 49.8132 /CMR6 rf /Fd 174[73 77[32 32
2[{}3 74.7198 /CMEX10 rf /Fe 147[20 33 31[51 63[40 11[{}4
49.8132 /CMMI6 rf /Ff 145[43 1[21 46[60 10[38 1[38 6[30
30 40[{}7 74.7198 /CMR9 rf /Fg 149[21 30 30 47[43 49[60
4[21 60{}7 74.7198 /CMSY9 rf /Fh 139[23 5[37 51 20 31
24 22 29[47 75[{}8 41.511 /CMMI5 rf /Fi 211[65 44[{}1
83.022 /MSAM10 rf /Fj 129[38 4[38 44 9[46 1[23 40 29[74
4[64 4[55 4[60 2[21 21 27[46 11[36 6[49 11[{}15 74.7198
/CMMI9 rf /Fk 190[67 65[{}1 74.7198 /CMBX9 rf /Fl 144[55
55 4[39 39 13[46 106 120 6[78 88 76[35 35 38 38{}13 83.022
/CMEX10 rf /Fm 190[72 65[{}1 83.022 /CMBX10 rf /Fn 135[37
13[23 32 32 42 42 24[100 6[60 19[55 2[65 22[65 3[65 13[65
4[23 65{}15 83.022 /CMSY10 rf /Fo 135[44 7[46 1[46 1[23
6[37 7[23 1[23 29[65 8[42 42 42 42 42 4[65 1[32 32 17[42
12[65 6[65 2[{}19 83.022 /CMR10 rf /Fp 134[37 4[25 29
33 2[37 42 62 21 2[21 42 2[33 1[33 15[42 2[46 58 1[71
50 3[58 58 2[54 68[{TeXBase1Encoding ReEncodeFont}20
74.7198 /Times-Bold rf /Fq 133[29 33 33 50 33 37 21 29
29 1[37 37 37 54 21 1[21 21 37 37 21 33 37 33 37 37 11[54
42 37 46 1[46 1[50 62 42 1[33 25 1[54 3[50 46 46 11[37
37 37 1[37 2[19 25 3[25 25 40[{TeXBase1Encoding ReEncodeFont}46
74.7198 /Times-Italic rf /Fr 144[33 2[19 4[33 41[51 2[19
5[33 1[33 33 33 4[51 1[26 26 39[41{}13 58.1154 /CMR7
rf /Fs 134[34 38 3[25 2[30 2[41 59 21 35 27 23 39 32
4[29 13[39 5[53 63 46 2[29 8[35 4[20 40[32 3[30 14[{}22
58.1154 /CMMI7 rf /Ft 129[42 4[41 47 3[30 2[37 42 3[25
43 34 29 48 2[39 43 1[36 44 7[48 69 2[57 49 2[66 3[81
57 2[36 6[63 62 3[42 1[23 23 27[49 4[47 6[39 3[37 2[53
11[{}33 83.022 /CMMI10 rf /Fu 207[18 47[45{}2 41.511
/CMSY5 rf /Fv 194[43 11[28 28 4[43 1[22 22 40[{}6 41.511
/CMR5 rf /Fw 134[37 37 1[37 42 23 32 32 1[42 42 42 60
23 37 1[23 42 42 23 37 42 37 42 42 11[60 1[42 2[51 11[60
1[51 13[42 1[42 42 3[28 21 41[42 2[{TeXBase1Encoding ReEncodeFont}33
83.022 /Times-Italic rf /Fx 198[25 25 25 25 25 25 25
25 25 49[{TeXBase1Encoding ReEncodeFont}9 49.8132 /Times-Roman
rf /Fy 105[37 1[33 33 24[33 37 37 54 37 37 21 29 25 37
37 37 37 58 21 37 21 21 37 37 25 33 37 33 37 33 3[25
1[25 46 54 54 71 54 54 46 42 50 1[42 54 54 66 46 54 29
25 54 54 42 46 54 50 50 54 6[21 37 37 37 37 37 37 37
37 37 37 1[19 25 19 2[25 25 25 35[42 42 2[{
TeXBase1Encoding ReEncodeFont}75 74.7198 /Times-Roman
rf /Fz 252[32 2[48{}2 49.8132 /CMSY6 rf /FA 139[16 23
19 1[29 1[29 45 16 2[16 29 29 19 26 1[26 29 26 16[32
2[52 4[42 2[36 42 10[29 29 29 29 29 29 29 29 29 29 1[15
4[19 19 40[{TeXBase1Encoding ReEncodeFont}33 58.1154
/Times-Roman rf /FB 134[50 50 72 50 55 33 39 44 55 55
50 55 83 28 55 1[28 55 50 33 44 55 44 55 50 10[72 1[66
1[72 1[61 1[72 94 3[39 1[78 1[66 72 72 1[72 6[33 3[50
50 50 50 50 50 49[{TeXBase1Encoding ReEncodeFont}43 99.6264
/Times-Bold rf /FC 134[50 50 50 50 50 1[50 50 1[50 50
50 1[50 50 1[50 1[50 1[50 50 50 50 50 32[50 17[50 46[{
TeXBase1Encoding ReEncodeFont}21 83.022 /Courier rf /FD
107[37 37 24[37 42 42 60 42 42 23 32 28 42 42 42 42 65
23 42 23 23 42 42 28 37 42 37 42 37 3[28 1[28 2[60 78
60 60 51 46 55 1[46 60 60 74 51 60 32 28 60 60 46 51
60 55 55 60 1[37 3[23 23 42 42 42 42 42 42 42 42 42 42
23 21 28 21 2[28 28 28 1[69 33[46 46 2[{TeXBase1Encoding ReEncodeFont}
76 83.022 /Times-Roman rf /FE 207[19 44[34 52 1[52{}4
58.1154 /CMSY7 rf /FF 133[37 42 1[60 42 46 28 32 37 46
46 42 46 69 23 46 1[23 46 42 28 37 46 37 46 42 8[60 83
60 60 1[46 60 1[51 65 1[78 55 65 1[32 65 65 1[55 60 60
55 60 6[28 4[42 1[42 42 42 2[21 28 3[28 28 37[46 2[{
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4369 y(component)14 b(of)i(the)g FF(LOGOS)g FD([20)o(])1806
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2 1 bop 749 83 a FD(tract)20 b(a)h(fe)n(w)f(unkno)n(wn)e(ones,)i(from)f
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173 y Fw(e)o(ven-skipped)e FD(gene)h(gi)n(v)o(en)g(no)h(kno)n(wledge)e
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1021 y(whereas)28 b(the)h(rest)g(of)g(the)f(genome,)h(besides)g
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1292 y(kno)n(wn)30 b(as)i(the)f FF(cis-r)o(egulatory)e(system)p
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1563 y(of)20 b(comple)o(x)e(or)o(ganisms)g([4].)450 1674
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1855 y(tection.)56 b(Although)29 b(these)i(algorithms)f(w)o(ork)g(well)
i(for)e(simple)h(motif)f(patterns,)j(often)d(the)o(y)g(are)450
1946 y(incapable)18 b(of)i(distinguishing)d(what)j(biologists)f(w)o
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2036 y(recurring)14 b(pattern)h([5)o(],)i(and)e(pro)o(vide)f(almost)i
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2126 y(edge)h(of)h(motif)f(structure)g(and)h(sequence)e(composition.)22
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2217 y(objecti)n(v)o(e)20 b(functions)f(for)h(motif)h(detection.)26
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2398 y(binding)27 b(between)h(multiple)h(transcription)e(f)o(actors)58
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y(the)16 b(motif)f(patterns)g(and)h(incorporating)c(gene)j(e)o
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(ferent)f(motif)h(patterns)f(may)450 3121 y(restrict)c(its)i(sensiti)n
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3232 y(T)-7 b(o)41 b(our)f(kno)n(wledge,)k(most)c(motif)h(models)f
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3323 y(monomer)33 b(distrib)n(utions)i(\(often)g(represented)f(as)i(a)g
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3503 y(in)e(the)g(motifs)g(\(possibly)e(with)i(the)g(e)o(xpection)e(of)
i([8)o(]\).)36 b(Such)23 b(strate)o(gies)h(contradict)e(our)i
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450 3684 y(in)i(practice)f(could)f(f)o(ail)i(to)g(distinguish)e
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4227 y(puting)c(motif)h(models)f(for)h(comple)o(x)e(biopolymer)g
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4408 y(Mark)o(o)o(v)23 b(Dirichlet-Multinomial)g(\(HMDM\))h(model,)h(w)
o(as)g(introduced)e(to)i(model)f(comple)o(x)f(motif)450
4498 y(patterns)h([19)o(].)38 b(HMDM)24 b(is)i(based)e(on)g(a)h
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3 2 bop 450 83 a FD(learned)19 b(from)g(databases)h(of)g(kno)n(wn)f
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49 b(In)28 b(other)f(w)o(ords,)i(conserv)o(ed)d(\()p
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1822 y(T)m(raditional)27 b(models)h(such)g(as)h(the)g(product)d
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450 1912 y(in)h(this)h(paper)e(for)g(details\))h(used)g(by)g(MEME)f
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2002 y(ing)p FD(:)24 b(gi)n(v)o(en)16 b(a)j(length)e
Ft(L)h FD(motif)f(for)h(which)f(only)1871 1970 y Fs(L)p
1871 1984 46 4 v 1877 2031 a Fr(2)1945 2002 y FD(positions)h(are)g
(conserv)o(ed,)e(PM)i(w)o(ould)f(assign)i(the)450 2093
y(same)d(probability)f(re)o(gardless)f(of)j(the)f(locations)f(of)i(the)
f(conserv)o(ed)e(sites.)25 b(A)17 b(possible)f(w)o(ay)g(to)g(model)450
2183 y(these)27 b(patterns)e(is)j(to)e(enforce)f Fw(a)h(priori)h
FD(a)g(')-5 b(shape')25 b(constraint)h(on)g(the)g(PWM)h(by)f
(introducing)e(ap-)450 2274 y(propriate)17 b(penalties)i(for)f
(patterns)h(violating)f(the)h(constraint.)k(This)c(is)h(a)g(highly)e
(ef)n(fecti)n(v)o(e)f(technique)450 2364 y(and)25 b(it)h(is)h(possible)
e(to)h(achie)n(v)o(e)e(high)h(speci\002city)g(with)h(the)f(aid)h(of)f
(carefully)f(designed)h(constraint)450 2454 y(functions)d(\(e.g.)33
b(where)22 b(the)h(')p Fv(+)o FD(')h(sites)g(are)f(e)o(xpected)e(to)j
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Fv(+)o FD(')450 2545 y(and)e(')p Fu(\000)o FD(')h(stretches,)f(etc.,)h
(see)g([11)n(])g(in)f(this)h(issue)g(for)f(an)g(ele)o(gant)f(algorithm)
f(that)j(solv)o(es)f(these)g(con-)450 2635 y(strained)g(models\).)26
b(HMDM)21 b(tak)o(es)h(a)f(v)o(ery)f(dif)n(ferent)g(approach.)25
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2726 y(shape)28 b(constraints,)i(rather)m(,)f(it)h(uses)f(Dirichlet)f
(distrib)n(utions)g(to)h(de\002ne)f(prototypes)f(\(each)h(corre-)450
2816 y(sponding)e(to)i(a)g(state)h(in)f(a)g(hidden)f(Mark)o(o)o(v)f
(chain\))h(of)h(possible)f(conserv)o(ed)f(and)h(heterogeneous)450
2907 y(nt-distrib)n(utions)21 b(so)i(that)g(each)g(particular)e(motif)h
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Fv(+++)m FD(')23 b(or)g(')p Fv(+)p Fu(\000)p Fv(+)p Fu(\000)p
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2997 y(is)i(represented)d(by)h(a)h(state)h(sequence)e(in)h(the)g
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(con\002gurations)e(of)i(the)g(state)h(sequences.)36
b(Preference)450 3178 y(for)23 b(the)g(characteristic)g(motif)g(shapes)
g(is)h(implicitly)f(encoded)f(in)i(the)f(distrib)n(ution)f(of)i(the)f
(state)h(se-)450 3268 y(quences,)18 b(which)g(depends)g(on)g(both)g
(the)h(observ)o(ed)e(DN)m(A)i(sequences)f(to)h(be)g(analyzed)e(and)i
(the)g(prior)450 3359 y(kno)n(wledge)f(incorporated)f(in)k(the)f(HMDM.)
g(Thus,)f(during)g(motif)h(detection,)e(we)j(actually)f(perform)450
3449 y(Bayesian)g(estimation)f(of)h(the)g(motif)f(model,)g(a)n(v)o
(eraging)f(o)o(v)o(er)g(all)j(possible)e(shape)h(patterns)f(accord-)450
3539 y(ing)h(to)g(their)g(posterior)f(probabilities)g(rather)g(than)h
(focusing)f(on)h(a)g(single,)g(prescribed)f(motif)g(shape.)450
3630 y(As)24 b(we)g(will)g(see)g(later)g(in)f(this)h(paper)m(,)f(our)f
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(xist.)450 3922 y(It)h(is)h(note)n(w)o(orthy)c(that)i(motif)h
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(local)h(constraints)450 4012 y(on)f(motif)f(')-5 b(shapes')19
b(is)g(only)g(part)f(of)h(the)g(issue.)25 b(As)20 b(pointed)d(out)i(in)
g(our)f(earlier)h(methodological)d(pa-)450 4103 y(pers)j([19)o(,)h(20)o
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(wing)f(tw)o(o)i(components,)d(the)j Fw(local)450 4193
y(alignment)e(model)p FD(,)i(which)f(models)g(the)h(PWM)g(of)g
(multi-aligned)e(motif)h(instances;)h(and)f(the)h Fw(global)450
4283 y(distrib)n(ution)28 b(model)p FD(,)j(which)d(characterizes)g(the)
g(distrib)n(ution)g(of)h(motif)f(instances)h(in)g(sequences.)450
4374 y(Both)21 b(components)f(can)h(e)o(xpress)f(rich)i(semantics)f(b)n
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b(In)450 4464 y(this)18 b(paper)m(,)f(we)h(primarily)e(focus)h(on)h
(the)f Fw(local)h(alignment)e(model)h FD(and)g(for)h(simplicity)-5
b(,)17 b(adopt)g(a)h(v)o(ery)p 450 4534 1196 4 v 555
4589 a Fx(2)584 4621 y Fy(The)27 b(characteristic)g(conserv)n(ation)i
(pattern)e(of)f(the)h(sites)g(in)f(a)h(motif)f(is)h(often)g
(re\003ected)g(in)f(the)h(')l(shape')450 4703 y(\(e.g.)j
Fq(U-)21 b(or)h(bell-shaped)p Fy(\))g(of)g(the)f
(information-content-plot)i(of)e(the)h(PWM)e(of)i(the)f(motif)g(\(e.g.)
30 b(Figure)21 b(1\))h(or)450 4786 y(the)h(contour)h(of)f(the)f(motif)h
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b(is)g(important)i(to)e(remember)i(that)e(')l(shape')i(is)e(only)450
4868 y(associated)16 b(to)g(the)g(conserv)n(ation)h(pattern)f(in)f(PWM)
g(of)h(a)f(motif,)h(b)o(ut)f Fp(not)g Fy(to)h(an)o(y)g(speci\002c)g
(consensus)h(sequences)450 4950 y(of)i(the)g(motif.)p
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%%Page: 4 4
4 3 bop 450 83 a FD(simple)24 b Fw(global)f(distrib)n(ution)g(model)p
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667 y(\(Figure)19 b(1\))i(.)26 b(Each)20 b(motif)g(typically)g(appears)
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1140 y Ft(;)14 b(:)g(:)g(:)f(;)h(y)3287 1152 y Fs(T)3339
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1781 y(multi-alignment.)e(W)-7 b(e)20 b(denote)d(the)i(multi-alignment)
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1872 y(indicator)f(string)g Ft(x)i FD(in)f(sequence)f
Ft(y)k FD(by)d Fm(A)p Fo(\()p Ft(x;)14 b(y)s Fo(\))p
FD(.)26 b(Since)19 b(an)o(y)f Fm(A)p Fo(\()p Ft(x;)c(y)s
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1464 2085 y Fs(l)p Fr(4)1523 2073 y Fn(i)24 b FD(is)g(an)f(inte)o(ger)f
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2563 y Fs(l)1409 2551 y Fo(=)33 b Fn(h)p Ft(\022)1578
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1020 y Fs(l)1565 1008 y Fo(\))p FD(,)28 b(which)d(determines)g(the)h
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14 28 14 52 14 134 14 -214 14 0 14 -20 13 11 14 -11
14 154 14 -106 14 19 14 -56 2339 1223 77 MP stroke
14 -107 14 67 14 -17 13 -22 14 19 14 -56 14 9 14 174
14 -67 14 -107 13 -12 14 3 14 59 14 84 14 0 14 13
13 -147 14 28 14 52 14 134 14 -214 14 0 14 -20 13 11
14 -11 14 154 14 -106 14 19 14 -56 2339 1223 30 MP stroke
SO
c9
14 0 13 -201 14 -347 14 -40 14 -17 14 233 14 -216 13 253
14 -95 14 -56 14 -56 14 56 14 -22 14 382 13 126 14 0
2755 559 17 MP stroke
gr
c9
24 W
2755 559 PD
24 W
2769 559 PD
24 W
2782 685 PD
24 W
2796 1067 PD
24 W
2810 1045 PD
24 W
2824 1101 PD
24 W
2838 1045 PD
24 W
2852 989 PD
24 W
2866 894 PD
24 W
2879 1147 PD
24 W
2893 931 PD
24 W
2907 1164 PD
24 W
2921 1147 PD
24 W
2935 1107 PD
24 W
2949 760 PD
24 W
2962 559 PD
24 W
2976 559 PD
gs 2326 389 1081 852 MR c np
DO
c8
14 197 14 -158 14 -28 14 -39 14 31 13 -51 14 11 14 25
14 15 14 36 14 -51 13 -16 14 216 14 -216 14 0 14 28
14 -28 14 -20 13 67 14 0 14 100 14 27 14 -49 14 -109
13 12 14 61 14 136 14 -158 14 52 2990 1095 30 MP stroke
gr
c8
DO
0 sg
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 96 FMSR
2678 328 mt
(gal4 \(14\)) s
SO
1 sg
0 852 1080 0 0 -852 3752 1240 4 MP
PP
-1080 0 0 852 1080 0 0 -852 3752 1240 5 MP stroke
4 w
DO
SO
6 w
0 sg
3752 1240 mt 4832 1240 L
3752 388 mt 4832 388 L
3752 1240 mt 3752 388 L
4832 1240 mt 4832 388 L
3752 1240 mt 4832 1240 L
3752 1240 mt 3752 388 L
3752 1240 mt 3752 1229 L
3752 389 mt 3752 399 L
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 72 FMSR
3732 1341 mt
(0) s
4074 1240 mt 4074 1229 L
4074 389 mt 4074 399 L
4034 1341 mt
(20) s
4396 1240 mt 4396 1229 L
4396 389 mt 4396 399 L
4356 1341 mt
(40) s
4719 1240 mt 4719 1229 L
4719 389 mt 4719 399 L
4679 1341 mt
(60) s
3752 1240 mt 3762 1240 L
4832 1240 mt 4821 1240 L
3677 1266 mt
(0) s
3752 899 mt 3762 899 L
4832 899 mt 4821 899 L
3677 925 mt
(1) s
3752 559 mt 3762 559 L
4832 559 mt 4821 559 L
3677 585 mt
(2) s
3752 1240 mt 4832 1240 L
3752 388 mt 4832 388 L
3752 1240 mt 3752 388 L
4832 1240 mt 4832 388 L
gs 3752 389 1081 852 MR c np
DO
c8
12 98 3768 1143 2 MP stroke
0 1 16 28 8 -29 3792 1241 4 MP stroke
6 16 4 -16 3860 1241 3 MP stroke
6 29 8 -29 3905 1241 3 MP stroke
9 31 17 -9 16 -6 4 -16 3989 1241 5 MP stroke
16 -30 16 37 16 -48 16 53 16 -53 16 99 16 -99 17 59
16 -78 16 57 16 -4 16 25 16 -74 16 63 16 -54 17 -9
16 18 16 74 16 -63 16 -43 16 82 16 -50 16 16 16 -19
17 47 16 84 16 -131 16 128 16 4 16 -4 16 435 16 -274
17 359 16 -85 16 85 16 -605 16 5 16 -42 16 -15 16 -10
17 13 16 8 16 -2 16 0 16 -29 3 -5 4087 1241 47 MP stroke
12 98 3768 1143 2 MP stroke
0 1 16 28 8 -29 3792 1241 4 MP stroke
6 16 4 -16 3860 1241 3 MP stroke
6 29 8 -29 3905 1241 3 MP stroke
9 31 17 -9 16 -6 4 -16 3989 1241 5 MP stroke
16 5 16 -42 16 -15 16 -10 17 13 16 8 16 -2 16 0
16 -29 3 -5 4087 1241 11 MP stroke
SO
c9
16 435 16 -274 17 359 16 -85 16 85 4251 559 6 MP stroke
gr
c9
24 W
4251 559 PD
24 W
4267 644 PD
24 W
4283 559 PD
24 W
4300 918 PD
24 W
4316 644 PD
24 W
4332 1079 PD
gs 3752 389 1081 852 MR c np
DO
c8
16 -30 16 37 16 -48 16 53 16 -53 16 99 16 -99 17 59
16 -78 16 57 16 -4 16 25 16 -74 16 63 16 -54 17 -9
16 18 16 74 16 -63 16 -43 16 82 16 -50 16 16 16 -19
17 47 16 84 16 -131 16 128 16 4 4348 1075 30 MP stroke
gr
c8
DO
0 sg
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 96 FMSR
4090 328 mt
(gcn4 \(24\)) s
SO
1 sg
0 852 1080 0 0 -852 5179 1240 4 MP
PP
-1080 0 0 852 1080 0 0 -852 5179 1240 5 MP stroke
4 w
DO
SO
6 w
0 sg
5179 1240 mt 6259 1240 L
5179 388 mt 6259 388 L
5179 1240 mt 5179 388 L
6259 1240 mt 6259 388 L
5179 1240 mt 6259 1240 L
5179 1240 mt 5179 388 L
5179 1240 mt 5179 1229 L
5179 389 mt 5179 399 L
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 72 FMSR
5159 1341 mt
(0) s
5506 1240 mt 5506 1229 L
5506 389 mt 5506 399 L
5466 1341 mt
(20) s
5833 1240 mt 5833 1229 L
5833 389 mt 5833 399 L
5793 1341 mt
(40) s
6160 1240 mt 6160 1229 L
6160 389 mt 6160 399 L
6120 1341 mt
(60) s
5179 1240 mt 5189 1240 L
6259 1240 mt 6248 1240 L
5104 1266 mt
(0) s
5179 899 mt 5189 899 L
6259 899 mt 6248 899 L
5104 925 mt
(1) s
5179 559 mt 5189 559 L
6259 559 mt 6248 559 L
5104 585 mt
(2) s
5179 1240 mt 6259 1240 L
5179 388 mt 6259 388 L
5179 1240 mt 5179 388 L
6259 1240 mt 6259 388 L
gs 5179 389 1081 852 MR c np
DO
c8
16 -139 17 13 16 5 16 5 17 -23 16 -23 16 56 17 88
16 -6 16 -138 17 -7 16 30 17 43 16 -66 16 0 17 61
16 -55 16 156 17 -96 16 -73 16 30 17 84 16 -83 17 32
16 144 16 -6 17 -32 16 -149 16 232 17 426 16 0 16 0
17 -178 16 68 17 -527 16 166 16 -21 17 -55 16 -101 16 97
17 -97 16 13 16 -36 17 41 16 -41 17 88 16 -95 16 63
17 -56 16 23 16 -23 17 24 16 -31 16 13 17 -13 16 62
17 36 16 71 16 -156 17 55 16 -38 16 -10 17 21 16 -34
5195 1230 65 MP stroke
16 166 16 -21 17 -55 16 -101 16 97 17 -97 16 13 16 -36
17 41 16 -41 17 88 16 -95 16 63 17 -56 16 23 16 -23
17 24 16 -31 16 13 17 -13 16 62 17 36 16 71 16 -156
17 55 16 -38 16 -10 17 21 16 -34 5195 1230 30 MP stroke
SO
c9
16 0 16 0 17 -178 16 68 5686 669 5 MP stroke
gr
c9
24 W
5686 669 PD
24 W
5702 737 PD
24 W
5719 559 PD
24 W
5735 559 PD
24 W
5751 559 PD
gs 5179 389 1081 852 MR c np
DO
c8
16 -139 17 13 16 5 16 5 17 -23 16 -23 16 56 17 88
16 -6 16 -138 17 -7 16 30 17 43 16 -66 16 0 17 61
16 -55 16 156 17 -96 16 -73 16 30 17 84 16 -83 17 32
16 144 16 -6 17 -32 16 -149 16 232 5768 985 30 MP stroke
gr
c8
DO
0 sg
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 96 FMSR
5528 328 mt
(gcr1 \(17\)) s
SO
1 sg
0 852 1080 0 0 -852 899 2365 4 MP
PP
-1080 0 0 852 1080 0 0 -852 899 2365 5 MP stroke
4 w
DO
SO
6 w
0 sg
899 2365 mt 1979 2365 L
899 1513 mt 1979 1513 L
899 2365 mt 899 1513 L
1979 2365 mt 1979 1513 L
899 2365 mt 1979 2365 L
899 2365 mt 899 1513 L
899 2365 mt 899 2354 L
899 1513 mt 899 1523 L
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 72 FMSR
879 2466 mt
(0) s
1207 2365 mt 1207 2354 L
1207 1513 mt 1207 1523 L
1167 2466 mt
(20) s
1516 2365 mt 1516 2354 L
1516 1513 mt 1516 1523 L
1476 2466 mt
(40) s
1824 2365 mt 1824 2354 L
1824 1513 mt 1824 1523 L
1784 2466 mt
(60) s
899 2365 mt 909 2365 L
1979 2365 mt 1968 2365 L
824 2391 mt
(0) s
899 2024 mt 909 2024 L
1979 2024 mt 1968 2024 L
824 2050 mt
(1) s
899 1683 mt 909 1683 L
1979 1683 mt 1968 1683 L
824 1709 mt
(2) s
899 2365 mt 1979 2365 L
899 1513 mt 1979 1513 L
899 2365 mt 899 1513 L
1979 2365 mt 1979 1513 L
gs 899 1513 1081 853 MR c np
DO
c8
15 -14 16 125 15 -57 16 -114 15 36 15 82 16 -39 15 234
16 -234 15 234 16 134 15 -134 15 0 16 77 15 -56 16 193
15 -172 16 -241 15 413 15 -135 16 -392 15 217 16 110 15 -213
16 57 15 46 15 310 16 -193 15 0 16 334 15 -313 16 35
15 137 15 141 16 0 15 0 16 -221 15 80 16 -491 15 298
15 -288 16 14 15 78 16 -24 15 -114 16 171 15 -111 15 253
16 -253 15 97 16 6 15 -24 16 57 15 67 15 -184 16 84
15 -49 16 -114 15 79 16 -33 15 217 15 -263 16 14 15 157
16 -33 15 -81 16 114 15 -114 914 2294 69 MP stroke
15 298 15 -288 16 14 15 78 16 -24 15 -114 16 171 15 -111
15 253 16 -253 15 97 16 6 15 -24 16 57 15 67 15 -184
16 84 15 -49 16 -114 15 79 16 -33 15 217 15 -263 16 14
15 157 16 -33 15 -81 16 114 15 -114 914 2294 30 MP stroke
SO
c9
15 -313 16 35 15 137 15 141 16 0 15 0 16 -221 15 80
1377 1824 9 MP stroke
gr
c9
24 W
1377 1824 PD
24 W
1392 1904 PD
24 W
1408 1683 PD
24 W
1423 1683 PD
24 W
1439 1683 PD
24 W
1454 1824 PD
24 W
1469 1961 PD
24 W
1485 1996 PD
24 W
1500 1683 PD
gs 899 1513 1081 853 MR c np
DO
c8
15 -14 16 125 15 -57 16 -114 15 36 15 82 16 -39 15 234
16 -234 15 234 16 134 15 -134 15 0 16 77 15 -56 16 193
15 -172 16 -241 15 413 15 -135 16 -392 15 217 16 110 15 -213
16 57 15 46 15 310 16 -193 15 0 1516 2017 30 MP stroke
gr
c8
DO
0 sg
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 96 FMSR
1181 1452 mt
(mat-a2 \(12\)) s
SO
1 sg
0 852 1080 0 0 -852 2326 2365 4 MP
PP
-1080 0 0 852 1080 0 0 -852 2326 2365 5 MP stroke
4 w
DO
SO
6 w
0 sg
2326 2365 mt 3406 2365 L
2326 1513 mt 3406 1513 L
2326 2365 mt 2326 1513 L
3406 2365 mt 3406 1513 L
2326 2365 mt 3406 2365 L
2326 2365 mt 2326 1513 L
2326 2365 mt 2326 2354 L
2326 1513 mt 2326 1523 L
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 72 FMSR
2306 2466 mt
(0) s
2648 2365 mt 2648 2354 L
2648 1513 mt 2648 1523 L
2608 2466 mt
(20) s
2970 2365 mt 2970 2354 L
2970 1513 mt 2970 1523 L
2930 2466 mt
(40) s
3293 2365 mt 3293 2354 L
3293 1513 mt 3293 1523 L
3253 2466 mt
(60) s
2326 2365 mt 2336 2365 L
3406 2365 mt 3395 2365 L
2251 2391 mt
(0) s
2326 2024 mt 2336 2024 L
3406 2024 mt 3395 2024 L
2251 2050 mt
(1) s
2326 1683 mt 2336 1683 L
3406 1683 mt 3395 1683 L
2251 1709 mt
(2) s
2326 2365 mt 3406 2365 L
2326 1513 mt 3406 1513 L
2326 2365 mt 2326 1513 L
3406 2365 mt 3406 1513 L
gs 2326 1513 1081 853 MR c np
DO
c8
16 -8 16 103 16 87 16 -205 16 -12 16 -7 16 80 17 56
16 -99 16 275 16 -284 16 93 16 -4 16 -30 16 -50 17 127
16 -130 16 19 16 0 16 69 16 -115 16 209 16 -94 16 -139
17 182 16 -146 16 58 16 -8 16 11 16 332 16 237 16 0
17 0 16 0 16 -228 16 -344 16 89 16 -183 16 -8 16 18
17 26 16 23 16 -49 16 124 16 -64 16 -64 16 80 16 -80
16 98 17 -98 16 45 16 11 16 101 16 50 16 -60 16 -59
16 -84 17 60 16 -19 16 -59 16 78 16 -53 16 37 16 16
16 -70 2342 2349 66 MP stroke
16 89 16 -183 16 -8 16 18 17 26 16 23 16 -49 16 124
16 -64 16 -64 16 80 16 -80 16 98 17 -98 16 45 16 11
16 101 16 50 16 -60 16 -59 16 -84 17 60 16 -19 16 -59
16 78 16 -53 16 37 16 16 16 -70 2342 2349 30 MP stroke
SO
c9
16 237 16 0 17 0 16 0 16 -228 2825 1911 6 MP stroke
gr
c9
24 W
2825 1911 PD
24 W
2841 1683 PD
24 W
2857 1683 PD
24 W
2874 1683 PD
24 W
2890 1683 PD
24 W
2906 1920 PD
gs 2326 1513 1081 853 MR c np
DO
c8
16 -8 16 103 16 87 16 -205 16 -12 16 -7 16 80 17 56
16 -99 16 275 16 -284 16 93 16 -4 16 -30 16 -50 17 127
16 -130 16 19 16 0 16 69 16 -115 16 209 16 -94 16 -139
17 182 16 -146 16 58 16 -8 16 11 2922 2252 30 MP stroke
gr
c8
DO
0 sg
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 96 FMSR
2678 1452 mt
(mcb \(16\)) s
SO
1 sg
0 852 1080 0 0 -852 3752 2365 4 MP
PP
-1080 0 0 852 1080 0 0 -852 3752 2365 5 MP stroke
4 w
DO
SO
6 w
0 sg
3752 2365 mt 4832 2365 L
3752 1513 mt 4832 1513 L
3752 2365 mt 3752 1513 L
4832 2365 mt 4832 1513 L
3752 2365 mt 4832 2365 L
3752 2365 mt 3752 1513 L
3752 2365 mt 3752 2354 L
3752 1513 mt 3752 1523 L
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 72 FMSR
3732 2466 mt
(0) s
4052 2365 mt 4052 2354 L
4052 1513 mt 4052 1523 L
4012 2466 mt
(20) s
4352 2365 mt 4352 2354 L
4352 1513 mt 4352 1523 L
4312 2466 mt
(40) s
4652 2365 mt 4652 2354 L
4652 1513 mt 4652 1523 L
4612 2466 mt
(60) s
3752 2365 mt 3762 2365 L
4832 2365 mt 4821 2365 L
3677 2391 mt
(0) s
3752 2024 mt 3762 2024 L
4832 2024 mt 4821 2024 L
3677 2050 mt
(1) s
3752 1683 mt 3762 1683 L
4832 1683 mt 4821 1683 L
3677 1709 mt
(2) s
3752 2365 mt 4832 2365 L
3752 1513 mt 4832 1513 L
3752 2365 mt 3752 1513 L
4832 2365 mt 4832 1513 L
gs 3752 1513 1081 853 MR c np
DO
c8
15 -101 15 101 15 -151 15 152 15 -128 15 85 15 26 15 -46
15 -39 15 59 15 -70 15 85 15 -38 15 -86 15 27 15 260
15 -136 15 -65 15 65 15 -151 15 39 15 70 15 -59 15 101
15 -65 15 85 15 39 15 -124 15 38 15 214 15 89 15 -89
15 -51 15 0 15 51 15 0 15 322 15 0 15 0 15 0
15 -450 15 77 15 -237 15 121 15 -121 15 101 15 59 15 -171
15 85 15 -74 15 187 15 -187 15 -26 15 186 15 -75 15 -85
15 237 15 -248 15 326 15 -341 15 26 15 -26 15 0 15 348
15 -85 15 -287 15 50 15 39 15 -39 15 -11 3767 2304 71 MP stroke
15 77 15 -237 15 121 15 -121 15 101 15 59 15 -171 15 85
15 -74 15 187 15 -187 15 -26 15 186 15 -75 15 -85 15 237
15 -248 15 326 15 -341 15 26 15 -26 15 0 15 348 15 -85
15 -287 15 50 15 39 15 -39 15 -11 3767 2304 30 MP stroke
SO
c9
15 89 15 -89 15 -51 15 0 15 51 15 0 15 322 15 0
15 0 15 0 4217 1683 11 MP stroke
gr
c9
24 W
4217 1683 PD
24 W
4232 1683 PD
24 W
4247 1683 PD
24 W
4262 1683 PD
24 W
4277 2005 PD
24 W
4292 2005 PD
24 W
4307 2056 PD
24 W
4322 2056 PD
24 W
4337 2005 PD
24 W
4352 1916 PD
24 W
4367 2005 PD
gs 3752 1513 1081 853 MR c np
DO
c8
15 -101 15 101 15 -151 15 152 15 -128 15 85 15 26 15 -46
15 -39 15 59 15 -70 15 85 15 -38 15 -86 15 27 15 260
15 -136 15 -65 15 65 15 -151 15 39 15 70 15 -59 15 101
15 -65 15 85 15 39 15 -124 15 38 4382 2219 30 MP stroke
gr
c8
DO
0 sg
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 96 FMSR
4091 1452 mt
(mig1 \(11\)) s
SO
1 sg
0 852 1080 0 0 -852 5179 2365 4 MP
PP
-1080 0 0 852 1080 0 0 -852 5179 2365 5 MP stroke
4 w
DO
SO
6 w
0 sg
5179 2365 mt 6259 2365 L
5179 1513 mt 6259 1513 L
5179 2365 mt 5179 1513 L
6259 2365 mt 6259 1513 L
5179 2365 mt 6259 2365 L
5179 2365 mt 5179 1513 L
5179 2365 mt 5179 2354 L
5179 1513 mt 5179 1523 L
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 72 FMSR
5159 2466 mt
(0) s
5459 2365 mt 5459 2354 L
5459 1513 mt 5459 1523 L
5419 2466 mt
(20) s
5740 2365 mt 5740 2354 L
5740 1513 mt 5740 1523 L
5700 2466 mt
(40) s
6020 2365 mt 6020 2354 L
6020 1513 mt 6020 1523 L
5980 2466 mt
(60) s
5179 2365 mt 5189 2365 L
6259 2365 mt 6248 2365 L
5104 2391 mt
(0) s
5179 2024 mt 5189 2024 L
6259 2024 mt 6248 2024 L
5104 2050 mt
(1) s
5179 1683 mt 5189 1683 L
6259 1683 mt 6248 1683 L
5104 1709 mt
(2) s
5179 2365 mt 6259 2365 L
5179 1513 mt 6259 1513 L
5179 2365 mt 5179 1513 L
6259 2365 mt 6259 1513 L
gs 5179 1513 1081 853 MR c np
DO
c8
14 31 14 101 14 45 14 -152 14 43 14 -108 14 47 14 -62
14 71 14 -31 14 -57 14 58 14 -35 14 218 14 -67 14 -42
14 -21 14 44 14 -41 14 -5 14 40 14 -126 14 45 14 -45
14 100 14 -119 14 51 14 -2 14 -54 14 195 14 49 14 1
14 165 14 -127 14 -277 14 61 14 20 15 -68 14 -12 14 0
14 270 14 0 14 94 14 -25 14 64 14 -326 14 -1 14 125
14 -155 14 45 14 -70 14 111 14 -54 14 -50 14 60 14 -55
14 164 14 -97 14 -60 14 78 14 -116 14 115 14 -111 14 19
14 47 14 6 14 96 14 -177 14 4 14 20 14 55 14 46
14 -108 14 54 14 23 5193 2263 76 MP stroke
14 -1 14 125 14 -155 14 45 14 -70 14 111 14 -54 14 -50
14 60 14 -55 14 164 14 -97 14 -60 14 78 14 -116 14 115
14 -111 14 19 14 47 14 6 14 96 14 -177 14 4 14 20
14 55 14 46 14 -108 14 54 14 23 5193 2263 30 MP stroke
SO
c9
14 49 14 1 14 165 14 -127 14 -277 14 61 14 20 15 -68
14 -12 14 0 14 270 14 0 14 94 14 -25 14 64 5613 1951 16 MP stroke
gr
c9
24 W
5613 1951 PD
24 W
5627 2015 PD
24 W
5641 1990 PD
24 W
5655 2084 PD
24 W
5669 2084 PD
24 W
5683 2354 PD
24 W
5697 2354 PD
24 W
5711 2342 PD
24 W
5726 2274 PD
24 W
5740 2294 PD
24 W
5754 2355 PD
24 W
5768 2078 PD
24 W
5782 1951 PD
24 W
5796 2116 PD
24 W
5810 2117 PD
24 W
5824 2166 PD
gs 5179 1513 1081 853 MR c np
DO
c8
14 31 14 101 14 45 14 -152 14 43 14 -108 14 47 14 -62
14 71 14 -31 14 -57 14 58 14 -35 14 218 14 -67 14 -42
14 -21 14 44 14 -41 14 -5 14 40 14 -126 14 45 14 -45
14 100 14 -119 14 51 14 -2 14 -54 5838 2361 30 MP stroke
gr
c8
DO
0 sg
%%IncludeResource: font Helvetica
/Helvetica /ISOLatin1Encoding 96 FMSR
5542 1452 mt
(crp \(24\)) s
SO
end
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%%EndObject
epage
end
showpage
%%Trailer
%%EOF
%%EndDocument
@endspecial 450 673 a FD(Figure)28 b(1:)43 b Fy(Y)-7
b(east)26 b(motifs)g(\(solid)h(line\))f(with)g Fg(\006)g
Fy(30)450 755 y(bp)k(\003anking)h(re)o(gions)f(\(dashed)h(line\).)56
b(The)30 b Fj(x)f Fy(axis)450 837 y(inde)o(x)o(es)18
b(position)g(and)g(the)f Fj(y)i Fy(axis)f(represents)g(the)f(in-)450
919 y(formation)i(content)g Ff(2)c Fg(\000)f Fj(H)6 b
Ff(\()p Fj(\022)1264 928 y Fe(l)1287 919 y Ff(\))18 b
Fy(of)g(the)h(multinomial)450 1001 y(distrib)o(ution)24
b Fj(\022)853 1010 y Fe(l)901 1001 y Fy(of)g(nt)h(at)e(position)i
Fj(l)q Fy(.)39 b(Note)24 b(the)h(tw)o(o)450 1084 y(typical)19
b(patterns:)k(the)18 b Fq(U)p Fy(-shape)i(and)f(the)f
Fq(bell)p Fy(-shape.)2128 658 y @beginspecial 0 @llx
0 @lly 206 @urx 129 @ury 1296 @rwi @setspecial
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450 1214 y FD(determined,)27 b(and)g(that)h(each)g(prototype)d(is)k
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y Ft(;)646 b FD(\(4\))1308 3254 y Ft(p)p Fo(\()p Ft(q)s
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Fs(I)1863 3176 y Fl(Y)1862 3352 y Fs(i)p Fr(=1)1969 3254
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3220 y Fs(q)2123 3195 y Fh(i)2121 3237 y Fv(1)2171 3151
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Fs(i;j)2638 3254 y Fo(])2661 3218 y Fs(q)2693 3193 y
Fh(i)2691 3235 y(l)2720 3218 y Fs(q)2752 3190 y Fh(j)2750
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b(These)26 b(properties)f(relie)n(v)o(e)h(our)f(motif)h(model)g(from)f
(the)h(restricted,)450 806 y(often)19 b(brittle)g(constraints)g(needed)
f(in)i(other)f(models,)g(such)g(as)h(e)o(xactly)f(what)g(shape)h(to)f
(look)g(for)m(,)g(the)450 897 y(widths)27 b(of)g(the)h(conserv)o(ed)d
(and)i(unserv)o(ed)e(patches)i(in)g(a)h(motif,)g(the)g(length)e(of)h
(the)h(whole)e(motif,)450 987 y(etc.,)20 b(and)g(as)h(a)f(result)g(pro)
o(vide)f(desirable)g(\003e)o(xibility)h(and)f(rob)n(ustness.)450
1098 y(When)24 b(multiple)g(motifs)g(are)g(to)g(be)h(found,)e(the)h
(local)h(alignment)d(model)i(can)g(be)g(generalized)f(to)h(a)450
1189 y(mixture)h(of)h(HMDMs,)i(a)f(Bayesian)f(multinet)g(with)g(shared)
g(structure.)42 b(If)26 b(we)h(w)o(ant)f(to)g(introduce)450
1279 y(more)18 b(than)g(one)g(class)h(of)g(priors)e(for)h(the)h
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450 1370 y(tainties)k(about)f(the)h(Dirichlet)g(mixture)f(prior)g(and)g
(the)h(transition)f(model)g(\(which)g(might)h(be)g(indeed)450
1460 y(necessary)k(since)h(motifs)g(seem)g(to)g(ha)n(v)o(e)f(multiple)h
(shape)f(classes)i(\(Figure)e(1\)\),)i(then)e(we)h(need)f(to)450
1550 y(introduce)18 b(an)i(unobserv)o(ed)e Fw(c)o(hoice)h(variable)g
FD(and)h(another)f(layer)g(of)h(mixture)f([19)o(].)450
1740 y FF(3.3)82 b(Unif)n(orm)20 b(and)g(Independent)i(Start)d(P)n
(osition)h(\(UISP\))h(Model)f(of)g(Motif)g(Indicator)450
1886 y FD(The)e(HMDM)g(generati)n(v)o(e)f(process)g(only)h(creates)g
(aligned)f(multiple)h(instances)g(of)g(a)h(motif,)f(b)n(ut)g(does)450
1976 y(not)k(complete)g(the)h(generation)d(of)j(the)g(observ)o(ed)d
(sequence)i(set.)33 b(W)-7 b(e)24 b(need)e(a)h(model)f(for)g(the)h
(back-)450 2067 y(ground)f(sequences)h(and)h(another)e(process)i(that)g
(generates)f(the)h(positions)g(of)f(the)h(motif)g(instances.)450
2174 y(F)o(or)29 b(simplicity)-5 b(,)30 b(we)f(assume)g(a)h(simple)f
(global)f(nucleotide)g(frequenc)o(y)2664 2152 y Ft(~)2664
2174 y(\022)2703 2186 y Fr(0)2780 2174 y Fo(=)39 b(\()p
Ft(\022)2955 2186 y Fr(01)3025 2174 y Ft(;)14 b(:)g(:)g(:)g(;)g(\022)
3249 2186 y Fr(04)3319 2174 y Fo(\))30 b FD(as)450 2265
y(background)15 b(although)h(a)i(more)g(sophisticated)f(background)d
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2355 y(model,)i(can)h(be)g(trained)f(and)h(incorporated)d(with)k(no)f
(dif)n(\002culty)f(under)g(the)h FF(LOGOS)g FD(frame)n(w)o(ork.)450
2466 y(In)h(UISP)-9 b(,)22 b(the)f(motif)g(indicator)g
Ft(x)h FD(is)h(de\002ned)d(as)i(a)g(latent)g('address')e(v)n(ariable:)
27 b Ft(x)f Fo(=)f(\()p Ft(x)3053 2478 y Fr(1)3091 2466
y Ft(;)14 b(:)g(:)g(:)g(;)g(x)3323 2478 y Fs(M)3397 2466
y Fo(\))p FD(.)450 2557 y(Each)20 b(component)e Ft(x)1074
2569 y Fs(m)1158 2557 y FD(lies)j(in)f Fn(f)p Fo(1)p
Ft(;)14 b(:)g(:)g(:)f(;)h(T)30 b Fn(\000)18 b Ft(L)g
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g(motif.)450 2647 y Ft(M)32 b FD(is)25 b(the)e(total)h(number)d(of)i
(motif)g(instances)g([1)o(,)h(15)o(].)34 b(Gi)n(v)o(en)23
b(the)g(position-speci\002c)f(multinomial)450 2737 y(parameters)29
b Fo(\002)i FD(for)f(motifs)g(and)g(background,)f(the)h(joint)g
(probability)f(of)h(a)h(sequence)e Ft(y)34 b FD(and)c(the)450
2828 y(addresses)20 b Ft(x)h FD(of)f(motifs)g(therein)f(is:)881
3024 y Ft(p)p Fo(\()p Ft(x;)14 b(y)s Fn(j)p Fo(\002)1171
3036 y Fs(g)1209 3024 y Ft(;)g Fn(M)1346 3036 y Fs(g)1384
3024 y Fo(\))84 b Fn(/)1684 2920 y Fs(M)1666 2945 y Fl(Y)1647
3121 y Fs(m)p Fr(=1)1834 2920 y Fs(L)1804 2945 y Fl(Y)1804
3124 y Fs(l)p Fr(=1)1965 2920 y(4)1928 2945 y Fl(Y)1924
3122 y Fs(j)s Fr(=1)2053 2932 y Fl(h)2108 2968 y Ft(\022)2147
2980 y Fs(lj)p 2102 3005 108 4 v 2102 3081 a Ft(\022)2141
3093 y Fr(0)p Fs(j)2219 2932 y Fl(i)2258 2949 y Fs(h)2297
2958 y Fh(lj)2348 2949 y Fr(\()p Fs(y)r(;x)2468 2957
y Fh(m)2522 2949 y Fr(\))2571 3024 y Fn(\001)2653 2920
y Fr(4)2616 2945 y Fl(Y)2612 3122 y Fs(j)s Fr(=1)2741
2957 y Fl(\002)2775 3024 y Ft(\022)2814 3036 y Fr(0)p
Fs(j)2882 2957 y Fl(\003)2917 2974 y Fs(h)2956 2982 y
Fv(0)p Fh(j)450 3262 y FD(The)20 b(conditional)e(distrib)n(ution)h(of)h
(latent)g(v)n(ariable)f Ft(x)j FD(is)f(thus:)1391 3459
y Ft(p)p Fo(\()p Ft(x)p Fn(j)p Ft(y)s(;)14 b Fo(\002\))83
b(=)1981 3355 y Fs(M)1962 3380 y Fl(Y)1944 3555 y Fs(m)p
Fr(=1)2101 3459 y Ft(p)p Fo(\()p Ft(x)2222 3471 y Fs(m)2285
3459 y Fn(j)p Ft(y)s(;)14 b Fo(\002\))p Ft(;)585 3804
y FD(where)82 b Ft(p)p Fo(\()p Ft(x)992 3816 y Fs(m)1055
3804 y Fn(j)p Ft(y)s(;)14 b Fo(\002\))83 b(=)1702 3674
y Fl(Q)1780 3694 y Fs(L)1780 3761 y(l)p Fr(=1)1904 3674
y Fl(Q)1982 3694 y Fr(4)1982 3761 y Fs(j)s Fr(=1)2115
3669 y Fl(\002)2150 3736 y Ft(\022)2189 3748 y Fs(lj)2245
3736 y Ft(=\022)2326 3748 y Fr(0)p Fs(j)2393 3669 y Fl(\003)2428
3686 y Fs(h)2467 3695 y Fh(lj)2518 3686 y Fr(\()p Fs(y)r(;x)2638
3694 y Fh(m)2692 3686 y Fr(\))p 1496 3785 1432 4 v 1496
3827 a Fl(P)1584 3847 y Fs(T)9 b FE(\000)p Fs(L)p Fr(+1)1584
3914 y Fs(t)p Fr(=1)1832 3827 y Fl(Q)1910 3847 y Fs(L)1910
3914 y(l)p Fr(=1)2033 3827 y Fl(Q)2112 3847 y Fr(4)2112
3914 y Fs(j)s Fr(=1)2245 3822 y Fl(\002)2279 3889 y Ft(\022)2318
3901 y Fs(lj)2375 3889 y Ft(=\022)2456 3901 y Fr(0)p
Fs(j)2523 3822 y Fl(\003)2558 3839 y Fs(h)2597 3848 y
Fh(lj)2648 3839 y Fr(\()p Fs(y)r(;x)2768 3847 y Fh(m)2822
3839 y Fr(=)p Fs(t)p Fr(\))2938 3804 y Ft(:)450 4046
y FD(Essentially)-5 b(,)25 b(the)f(probability)f(of)h
Ft(x)1513 4058 y Fs(m)1602 4046 y FD(being)f(a)i(motif)f(start)h
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4136 y(hood)18 b(ratio)h(of)f(a)i(sub-sequence)d(of)i(length)f
Ft(L)h FD(started)g(at)h Ft(x)2180 4148 y Fs(m)2263 4136
y FD(being)e(a)i(motif)f(sequence)f(with)h(respect)450
4227 y(to)28 b(its)h(probability)d(of)i(being)f(a)i(background)c
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b(UISP)e(reduces)f(to)i(the)450 4317 y(well-kno)n(wn)18
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(instances,)i(or)f(a)h(range)f(for)g(the)450 4498 y(number)j(of)i
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4679 y(ing)d(intrinsic)g(features)g(of)h(motifs)f(which)g(can)g(help)g
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b(Once)450 4769 y(this)d(is)h(achie)n(v)o(ed,)f(we)g(can)g(readily)f
(inte)o(grate)f(the)i(model)f(as)h(a)g(component)e(into)h
FF(LOGOS)h FD([20)o(],)450 4860 y(which)18 b(supports)g(modular)e(e)o
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634 y FD(In)20 b(order)e(to)i(do)g(Bayesian)g(estimation)f(of)h(the)g
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(distrib)n(ution)h Ft(p)p Fo(\()p Ft(\022)r Fn(j)p Ft(y)s
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Ft(\022)r(;)14 b(q)s(;)g(x)p Fn(j)p Ft(y)s(;)g Fn(M)p
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Ft(x)p Fo(\))j FD(that)f(approximates)d Ft(p)p Fo(\()p
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1787 V 134 w(abf1\(mishit\))p 2158 1787 V 144 w(gal4\(hit\))p
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1987 4 v 937 1856 4 66 v 989 1836 a(HMDM)p 1391 1856
V 266 w(0.8095)p 1727 1856 V 176 w(0)p 2158 1856 V 401
w(0.9286)p 2494 1856 V 176 w(0)p 2924 1856 V 939 1859
1987 4 v 937 1925 4 66 v 989 1905 a(PM)g(\(MEME\))p 1391
1925 V 141 w(0)p 1727 1925 V 307 w(0.4762)p 2158 1925
V 270 w(0.1429)p 2494 1925 V 176 w(0.1429)p 2924 1925
V 939 1928 1987 4 v 450 2137 a FF(5.2.2)81 b(Generalizability)450
2269 y FD(Ho)n(w)31 b(well)g(does)f(HMDM)h(generalize?)55
b(W)-7 b(e)32 b(split)g(our)e(data)g(into)h(a)g(training)e(set)j(of)e
(12)h(motifs:)450 2359 y Fn(F)46 b Fo(=)37 b Fn(f)p Fw(mcm1,)20
b(pdr1,)f(pho2,)g(pho4,)f(r)o(ap1,)h(r)m(eb1,)h(r)m(ep,)g(r)l(ox1,)g
(scb,)g(ste12,)g(tbp,)g(uasphr)n Fn(g)p FD(,)30 b(and)e(a)h(test)450
2458 y(set)f(of)e(8)h(motifs)g(\(as)g(sho)n(wn)f(in)h(Figure)g(1\))1774
2428 y FA(9)1808 2458 y FD(.)45 b(Model)26 b(HMDM\(f\))g(w)o(as)i
(\002tted)f(on)g Fn(F)8 b FD(.)45 b(In)27 b(the)g(\002rst)450
2549 y(motif)20 b(\002nding)g(task,)h(we)h(use)f(synthetic)f(sequences)
g(each)h(ha)n(ving)f(only)g(one)g(true)h(motif)f(instance)h(at)450
2639 y(a)d(random)f(position.)23 b(T)-7 b(able)18 b(2)g(summarizes)f
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(sho)n(wn)450 2729 y(in)k(the)h(table,)f(the)h(HMDM\(f\))e(model)g
(signi\002cantly)h(outperforms)d(PM)k(for)f(motifs)g
Fw(abf1)p FD(,)g Fw(gal4)f FD(and)450 2820 y Fw(crp)p
FD(,)28 b(and)d(achie)n(v)o(es)g(comparable)g(performance)e(for)i
(motifs)h Fw(gcn4)f FD(and)h Fw(mig1)p FD(.)42 b(It)27
b(does)f(poorly)e(for)450 2910 y(motifs)17 b Fw(mat-a2)g
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3001 y(\223conserv)o(ed,)-6 b(\224)14 b(which)h(is)i(in)e(f)o(act)h
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b(this)h(problem)e(by)h(obtaining)e(other)i(HMDM)g(models)g(that)g(are)
h(biased)f(to)n(w)o(ard)f(such)h(speci\002c)450 3272
y(patterns)j(\(e.g.,)f(via)h(empirically)f(specifying)f(a)j(transition)
e(matrix)h Ft(B)k FD(for)c(the)g(HMDM,)g(or)g(training)450
3362 y(the)h(HMDM)g(on)g(another)f(training)g(set)h(structurally)f
(similar)i(to)f(the)g(motif)g(patterns)f(of)h(interest\),)g(a)450
3453 y(remedy)c(not)h(possible)f(for)h(motif)g(\002nding)f(algorithms)g
(using)g(the)i(PM)f(model.)450 3643 y(T)-7 b(able)23
b(2:)32 b Fy(Motif)21 b(detection)i(on)f(an)g(independent)h(test)f
(dataset:)29 b(median)22 b Fp(hit)p Fy(-rate)f(o)o(v)o(er)h(80)g(e)o
(xperiments)g(con-)450 3725 y(taining)d(only)h(true)f(motifs.)p
893 3753 2078 4 v 891 3818 4 66 v 1322 3818 V 1374 3799
a FA(abf1)p 1528 3818 V 103 w(gal4)p 1734 3818 V 105
w(gcn4)p 1940 3818 V 93 w(gcr1)p 2146 3818 V 103 w(mat)p
2352 3818 V 119 w(mcb)p 2558 3818 V 106 w(mig1)p 2764
3818 V 87 w(crp)p 2970 3818 V 893 3822 2078 4 v 891 3887
4 66 v 943 3868 a(HMDM\(f\))p 1322 3887 V 186 w(0.86)p
1528 3887 V 104 w(0.79)p 1734 3887 V 103 w(0.71)p 1940
3887 V 104 w(0.76)p 2146 3887 V 104 w(0)p 2352 3887 V
177 w(0.06)p 2558 3887 V 104 w(0.73)p 2764 3887 V 104
w(0.63)p 2970 3887 V 893 3891 2078 4 v 891 3957 4 66
v 943 3937 a(PM)c(\(MEME\))p 1322 3957 V 118 w(0.52)p
1528 3957 V 104 w(0.21)p 1734 3957 V 103 w(0.67)p 1940
3957 V 104 w(0.76)p 2146 3957 V 104 w(0.96)p 2352 3957
V 104 w(0.81)p 2558 3957 V 104 w(0.73)p 2764 3957 V 104
w(0.38)p 2970 3957 V 893 3960 2078 4 v 450 4112 a FD(In)23
b(task)g(one,)g(PM)g(sho)n(ws)g(a)g(decent)g(performance,)d(especially)
i(for)h(those)g(more-or)n(-less)e(uniformly)450 4202
y(conserv)o(ed)27 b(motifs)j(such)f(as)h Fw(gcn1)p FD(,)h
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(comple)o(x)f(shapes)i(\(e.g.)44 b Fw(gal4)p FD(\).)g(The)26
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b(\224)p 450 4444 1196 4 v 555 4499 a Fx(8)584 4531 y
Fy(By)21 b(permutation)h(we)e(mean)h(that)g(the)f(same)h(permuted)h
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(changed.)555 4672 y Fx(9)584 4703 y Fy(As)g(a)g(short)h(e)o
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(statistical)f(learning)i(technique,)g(this)f(setting)450
4786 y(is)i(called)g Fq(independent)i(validation)p Fy(,)f(for)f(which)g
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%%Page: 11 11
11 10 bop 450 83 a FD(T)-7 b(able)24 b(3)g(summarizes)f(the)i(median)e
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(permuted)450 625 y(v)o(ersion,)i(which)g(suggests)g(that)h(indeed)e
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(captured)f(by)450 716 y(HMDM\(f\),)e(consistent)h(with)g(the)g(result)
h(from)e(the)h(\002rst)h(task.)450 908 y(T)-7 b(able)21
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(dataset:)25 b(median)c Fp(hit)p Fy(-rate)d(\(top\))i(and)g
Fp(mishit)p Fy(-rate)f(\(bot-)450 991 y(tom\))g(o)o(v)o(er)g(80)g(e)o
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911 1042 2078 4 v 909 1108 4 66 v 1340 1108 V 1391 1088
a FA(abf1)p 1546 1108 V 103 w(gal4)p 1752 1108 V 106
w(gcn4)p 1958 1108 V 93 w(gcr1)p 2164 1108 V 103 w(mat)p
2369 1108 V 119 w(mcb)p 2575 1108 V 106 w(mig1)p 2781
1108 V 87 w(crp)p 2987 1108 V 911 1111 2078 4 v 909 1177
4 66 v 961 1157 a(HMDM\(f\))p 1340 1177 V 185 w(0.81)p
1546 1177 V 104 w(0.82)p 1752 1177 V 104 w(0.71)p 1958
1177 V 104 w(0.65)p 2164 1177 V 104 w(0)p 2369 1177 V
177 w(0)p 2575 1177 V 177 w(0.19)p 2781 1177 V 104 w(0.58)p
2987 1177 V 911 1180 2078 4 v 909 1246 4 66 v 961 1226
a(PM)14 b(\(MEME\))p 1340 1246 V 118 w(0.14)p 1546 1246
V 104 w(0)p 1752 1246 V 177 w(0)p 1958 1246 V 177 w(0.41)p
2164 1246 V 104 w(0.79)p 2369 1246 V 104 w(0.13)p 2575
1246 V 104 w(0.64)p 2781 1246 V 104 w(0.04)p 2987 1246
V 911 1249 2078 4 v 911 1296 V 909 1362 4 66 v 1340 1362
V 1391 1342 a(abf1)p 1546 1362 V 103 w(gal4)p 1752 1362
V 106 w(gcn4)p 1958 1362 V 93 w(gcr1)p 2164 1362 V 103
w(mat)p 2369 1362 V 119 w(mcb)p 2575 1362 V 106 w(mig1)p
2781 1362 V 87 w(crp)p 2987 1362 V 911 1365 2078 4 v
909 1431 4 66 v 961 1411 a(HMDM\(f\))p 1340 1431 V 185
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V 104 w(0.63)p 2575 1431 V 104 w(0)p 2781 1431 V 177
w(0.04)p 2987 1431 V 911 1435 2078 4 v 909 1500 4 66
v 961 1481 a(PM)g(\(MEME\))p 1340 1500 V 118 w(0.05)p
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1500 V 104 w(0.35)p 2164 1500 V 104 w(0)p 2369 1500 V
177 w(0.63)p 2575 1500 V 104 w(0)p 2781 1500 V 177 w(0.23)p
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(tweaking)g(is)i(in)m(v)n(olv)o(ed.)450 1749 y(The)23
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(Bayesian)g(learning)f(of)h(PWM)h(and)f(the)g(pos-)450
1840 y(terior)h(prediction)g(of)h(motif)f(locations)g(are)h(all)h
(automated.)38 b(Gi)n(v)o(en)24 b(such)h(little)h(human)e(ef)n(fort,)h
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2604 y(plain)f(construction)f(of)i(the)g(training)e(set.)43
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Fn(F)34 b FD(with)25 b(an)f(empirically)g(speci\002ed)450
3237 y(nearly)e(block-diagonal)e(matrix)j(that)g(embodies)f
Fw(site)i(clustering)f FD(for)f(the)h(transition)g(probabilities;)450
3327 y(HMDM\(b\),)17 b(deri)n(v)o(ed)f(with)j(a)f(training)f(set)i(of)f
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%%Page: 12 12
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450 586 y(Biologically)j(identi\002ed)f(motifs)h(include)g
Fw(bcd)p FD(,)i Fw(cad)p FD(,)f Fw(hb)p FD(,)h Fw(kni)f
FD(and)f Fw(kr)h FD([3)o(].)50 b(F)o(or)28 b(comparison,)g(we)450
677 y(pro)o(vide)e(the)i(PWMs)h(postulated)e(by)h(Berman)f
Fw(et)i(al)f FD(for)g(these)g(\002)n(v)o(e)g(motifs)f(as)i(used)f(in)g
([3)o(])h(for)e(a)450 767 y(motif)e(scan)h(task.)43 b(The)25
b(sources)g(of)h(all)h(PWMs)g(are)e(biologically)f(identi\002ed)i
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(motif,)g(and)h(about)450 948 y Fo(20)k Fn(\030)g Fo(40)c
FD(bases)h(in)f(length\).)30 b(The)22 b(PWMs)h(are)f(deri)n(v)o(ed)f
(from)g(an)h(alignment)f(of)h(all)h(such)f(instances)450
1038 y(of)h(a)h(motif)f(generated)f(by)h(MEME,)g(as)h(sho)n(wn)f(in)g
(Figure)g(4.)35 b(Note)24 b(that)f(these)h(PWMs)g(should)f(not)450
1129 y(be)28 b(tak)o(en)f(as)i(ground)c(truth.)47 b(Since)28
b(the)o(y)f(were)h(created)f(by)g(applying)f(MEME)i(to)g(collections)f
(of)450 1219 y(short,)e(motif-bearing)d(sequences,)j(both)f(the)h
(under)n(-representati)n(v)o(eness)c(of)k(the)g(data)f(source)g(\(e.g.)
450 1310 y Fw(kni)i FD(has)h(only)e(5)i(instances\))f(and)g(the)g
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%%EndDocument
@endspecial 1000 w @beginspecial 0 @llx 0 @lly 510 @urx
141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/factor_cad.fasta.eps
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% * seq_1
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% * seq_5
% * seq_6
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% * seq_8
% * seq_9
% * seq_10
% * seq_11
% * seq_12
% * seq_13
% * seq_14
% * seq_15
% * seq_16
% * seq_17
% * seq_18
% * seq_19
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% * seq_24
% * seq_25
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% * seq_27
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% * seq_60
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% * seq_96
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% * NUCLEOTIDE ALIGNMENT
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/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 10 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
(1) startstack
0.0183455572482361 (C) numchar
0.0366911144964723 (T) numchar
0.0372470404736915 (G) numchar
0.0744940809473831 (A) numchar
endstack
(2) startstack
0.00916621168189109 (C) numchar
0.018802485501315 (T) numchar
0.0190375165700815 (A) numchar
0.0235031068766438 (G) numchar
endstack
(3) startstack
0.00818833862956073 (C) numchar
0.00832257368906173 (G) numchar
0.00953068922457069 (A) numchar
0.0142289163071055 (T) numchar
endstack
(4) startstack
0.0321509672165251 (G) numchar
0.0401887090206563 (A) numchar
0.0544780277835563 (T) numchar
0.141107022783638 (C) numchar
endstack
(5) startstack
0.016600582423535 (T) numchar
0.0191063307138799 (C) numchar
0.019419549250173 (G) numchar
0.0388390985003459 (A) numchar
endstack
(6) startstack
0.0779491408105151 (G) numchar
0.17610731812746 (C) numchar
0.612045105623304 (T) numchar
endstack
(7) startstack
2 (A) numchar
endstack
(8) startstack
2 (A) numchar
endstack
(9) startstack
2 (A) numchar
endstack
(10) startstack
0.0225623547280353 (C) numchar
0.0459924923302257 (T) numchar
0.0616125840650194 (G) numchar
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endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 890 1787 a(bcd)881 b(cad)500 2063 y @beginspecial
0 @llx 0 @lly 510 @urx 141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/factor_hb.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
% * seq_4
% * seq_5
% * seq_6
% * seq_7
% * seq_8
% * seq_9
% * seq_10
% * seq_11
% * seq_12
% * seq_13
% * seq_14
% * seq_15
% * seq_16
% * seq_17
% * seq_18
% * seq_19
% * seq_20
% * seq_21
% * seq_22
% * seq_23
% * seq_24
% * seq_25
% * seq_26
% * seq_27
% * seq_28
% * seq_29
% * seq_30
% * seq_31
% * seq_32
% * seq_33
% * seq_34
% * seq_35
% * seq_36
% * seq_37
% * seq_38
% * seq_39
% * seq_40
% * seq_41
% * seq_42
% * seq_43
% * seq_44
% * seq_45
% * seq_46
% * seq_47
% * seq_48
% * seq_49
% * seq_50
% * seq_51
% * seq_52
% * seq_53
% * seq_54
% * seq_55
% * seq_56
% * seq_57
% * seq_58
% * seq_59
% * seq_60
% * seq_61
% * seq_62
% * seq_63
% * seq_64
% * seq_65
% * seq_66
% * seq_67
% * seq_68
% * seq_69
% * seq_70
% * seq_71
% * seq_72
% * seq_73
% * seq_74
% * seq_75
% * seq_76
% * seq_77
% * seq_78
% * seq_79
% * seq_80
% * seq_81
% * seq_82
% * seq_83
% * seq_84
% * seq_85
% * seq_86
% * seq_87
% * seq_88
% * seq_89
% * seq_90
% * seq_91
% * seq_92
% * seq_93
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 11 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
(1) startstack
0.0510955618516396 (G) numchar
0.0613146742219675 (C) numchar
0.0613146742219675 (A) numchar
0.301463814924674 (T) numchar
endstack
(2) startstack
2 (T) numchar
endstack
(3) startstack
0.0162466180450149 (A) numchar
0.0324932360900297 (G) numchar
0.0649864721800594 (C) numchar
1.39720915187128 (T) numchar
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(4) startstack
2 (T) numchar
endstack
(5) startstack
2 (T) numchar
endstack
(6) startstack
0.0205834120157473 (C) numchar
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(7) startstack
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endstack
(10) startstack
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endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 1000 w @beginspecial 0 @llx 0 @lly 510 @urx
141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/factor_kni.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
% * seq_4
% * seq_5
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 10 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
(1) startstack
2 (A) numchar
endstack
(2) startstack
2 (A) numchar
endstack
(3) startstack
0.125809881109066 (G) numchar
0.125809881109066 (A) numchar
0.377429643327199 (C) numchar
endstack
(4) startstack
0.411619762218133 (G) numchar
0.617429643327199 (T) numchar
endstack
(5) startstack
0.255614381022528 (C) numchar
1.02245752409011 (A) numchar
endstack
(6) startstack
2 (G) numchar
endstack
(7) startstack
0.125809881109066 (G) numchar
0.125809881109066 (C) numchar
0.377429643327199 (A) numchar
endstack
(8) startstack
0.0956143810225276 (C) numchar
0.191228762045055 (T) numchar
0.191228762045055 (G) numchar
endstack
(9) startstack
2 (C) numchar
endstack
(10) startstack
2 (A) numchar
endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 1000 w @beginspecial 0 @llx 0 @lly 510 @urx
141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/factor_kr.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
% * seq_4
% * seq_5
% * seq_6
% * seq_7
% * seq_8
% * seq_9
% * seq_10
% * seq_11
% * seq_12
% * seq_13
% * seq_14
% * seq_15
% * seq_16
% * seq_17
% * seq_18
% * seq_19
% * seq_20
% * seq_21
% * seq_22
% * seq_23
% * seq_24
% * seq_25
% * seq_26
% * seq_27
% * seq_28
% * seq_29
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 10 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
(1) startstack
0.0256124508815782 (T) numchar
0.0512249017631564 (C) numchar
0.0896435780855237 (G) numchar
0.204899607052626 (A) numchar
endstack
(2) startstack
0.0541028700353318 (G) numchar
0.0541028700353318 (C) numchar
1.46077749095396 (A) numchar
endstack
(3) startstack
0.0451484463588965 (T) numchar
0.13544533907669 (C) numchar
1.12871115897241 (A) numchar
endstack
(4) startstack
0.0289950607562243 (G) numchar
0.0386600810082991 (T) numchar
0.0676551417645234 (C) numchar
0.144975303781122 (A) numchar
endstack
(5) startstack
0.0615035540534047 (T) numchar
1.72209951349533 (G) numchar
endstack
(6) startstack
0.157258756177642 (A) numchar
1.36290922020623 (G) numchar
endstack
(7) startstack
0.0685747615356903 (C) numchar
0.171436903839226 (A) numchar
0.754322376892593 (G) numchar
endstack
(8) startstack
0.0615035540534047 (G) numchar
1.72209951349533 (T) numchar
endstack
(9) startstack
0.0262926332007347 (A) numchar
0.078877899602204 (C) numchar
0.105170532802939 (G) numchar
0.552145297215428 (T) numchar
endstack
(10) startstack
0.0294123920994624 (C) numchar
0.0882371762983872 (T) numchar
0.0882371762983872 (G) numchar
0.647072626188173 (A) numchar
endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 909 2083 a(hb)904 b(kni)d(kr)450 2181 y(Figure)25
b(4:)37 b Fy(Motif)24 b(patterns)g(in)g(the)h(re)o(gulatory)f(re)o
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b(The)24 b(motif)g(lo-)450 2263 y(gos)d(are)g(created)g(based)g(on)g
(multi-alignments)g(of)g(biologically)g(identi\002ed)g(motif)f
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b(e)18 b(use)h(a)g(modi\002ed)g(v)o(ersion)h(of)f(W)-6
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(wn,)c(and)i(apply)g FF(LOGOS)g FD([20)o(],)h(which)f(uses)h(a)g(HMDM)g
(\(the)f(one)g(sho)n(wn)450 2668 y(in)f(Figure)f(3\))h(as)h(the)f
(local)f(alignment)g(model,)g(b)n(ut)h(replaces)f(the)h(simple)g
(one-per)n(-sequence)c(model)450 2759 y(with)h(a)g(more)f(e)o(xpressi)n
(v)o(e)f(HMM)i(as)g(the)g(global)f(model)g(to)h(handle)e(the)i(comple)o
(x)e(issues)j(of)e(unkno)n(wn)450 2849 y(number)i(of)h(motif)g
(instances)g(and)g(simultaneous)f(detection)g(of)h(multiple)g(types)g
(of)g(motifs.)25 b(W)-7 b(e)20 b(also)450 2940 y(implemented)i(MEME,)g
(which)h(uses)h(the)g(PM)g(model,)f(for)g(comparison)f(\(on)g(the)i
(unannotated)d Fw(e)o(ve)450 3030 y FD(dataset)32 b(rather)f(than)g(on)
g(the)h(biologically)d(identi\002ed)i(short)h(motifs)f(se)o(gments)g
(from)f(which)i(the)450 3121 y(PWMs)21 b(in)g(Figure)e(4)i(were)f(deri)
n(v)o(ed\).)500 3488 y @beginspecial 0 @llx 0 @lly 510
@urx 141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/thetaI1.fake.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
% * seq_4
% * seq_5
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% * seq_164
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% * seq_198
% * seq_199
% * seq_200
% * seq_201
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% * seq_203
% * seq_204
% * seq_205
% * seq_206
% * seq_207
% * seq_208
% * seq_209
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% * seq_211
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% * seq_213
% * seq_214
% * seq_215
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% * seq_220
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% * seq_223
% * seq_224
% * seq_225
% * seq_226
% * seq_227
% * seq_228
% * seq_229
% * seq_230
% * seq_231
% * seq_232
% * seq_233
% * seq_234
% * seq_235
% * seq_236
% * seq_237
% * seq_238
% * seq_239
% * seq_240
% * seq_241
% * seq_242
% * seq_243
% * seq_244
% * seq_245
% * seq_246
% * seq_247
% * seq_248
% * seq_249
% * seq_250
% * seq_251
% * seq_252
% * seq_253
% * seq_254
% * seq_255
% * seq_256
% * seq_257
% * seq_258
% * seq_259
% * seq_260
% * seq_261
% * seq_262
% * seq_263
% * seq_264
% * seq_265
% * seq_266
% * seq_267
% * seq_268
% * seq_269
% * seq_270
% * seq_271
% * seq_272
% * seq_273
% * seq_274
% * seq_275
% * seq_276
% * seq_277
% * seq_278
% * seq_279
% * seq_280
% * seq_281
% * seq_282
% * seq_283
% * seq_284
% * seq_285
% * seq_286
% * seq_287
% * seq_288
% * seq_289
% * seq_290
% * seq_291
% * seq_292
% * seq_293
% * seq_294
% * seq_295
% * seq_296
% * seq_297
% * seq_298
% * seq_299
% * seq_300
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 15 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
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endstack
(3) startstack
0.00873899111550603 (A) numchar
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endstack
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0.0441773358950848 (A) numchar
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endstack
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endstack
(8) startstack
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endstack
(9) startstack
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endstack
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(11) startstack
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endstack
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endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 1000 w @beginspecial 0 @llx 0 @lly 510 @urx
141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/thetaII1.fake.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
% * seq_4
% * seq_5
% * seq_6
% * seq_7
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% * seq_251
% * seq_252
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% * seq_254
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% * seq_256
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% * seq_276
% * seq_277
% * seq_278
% * seq_279
% * seq_280
% * seq_281
% * seq_282
% * seq_283
% * seq_284
% * seq_285
% * seq_286
% * seq_287
% * seq_288
% * seq_289
% * seq_290
% * seq_291
% * seq_292
% * seq_293
% * seq_294
% * seq_295
% * seq_296
% * seq_297
% * seq_298
% * seq_299
% * seq_300
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 20 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
(1) startstack
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endstack
(2) startstack
0.00131202363189303 (G) numchar
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endstack
(3) startstack
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endstack
(4) startstack
0.0326273840483641 (G) numchar
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endstack
(5) startstack
0.0461451988205085 (C) numchar
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endstack
(6) startstack
0.0264177031535996 (G) numchar
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endstack
(7) startstack
0.0513639612035345 (G) numchar
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endstack
(8) startstack
0.0118395288048595 (G) numchar
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endstack
(9) startstack
0.0192696896641949 (C) numchar
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0.163792362145657 (A) numchar
endstack
(10) startstack
0.0214317733083169 (C) numchar
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endstack
(11) startstack
0.0255350404819369 (A) numchar
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endstack
(12) startstack
0.0189726309726411 (G) numchar
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0.0825867465867908 (A) numchar
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endstack
(13) startstack
0.017165040814105 (C) numchar
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endstack
(14) startstack
0.00681900182432641 (C) numchar
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endstack
(15) startstack
0.0109953961840642 (G) numchar
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endstack
(16) startstack
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endstack
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endstack
(20) startstack
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endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 1000 w @beginspecial 0 @llx 0 @lly 510 @urx
141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/thetaIII1.fake.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
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% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 10 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
(1) startstack
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1.8725374040768 (T) numchar
endstack
(2) startstack
0.0253045595145513 (A) numchar
1.8725374040768 (T) numchar
endstack
(3) startstack
0.0253045595145513 (A) numchar
1.8725374040768 (T) numchar
endstack
(4) startstack
0.0253045595145513 (A) numchar
1.8725374040768 (T) numchar
endstack
(5) startstack
0.0703083124367034 (A) numchar
1.68739949848088 (T) numchar
endstack
(6) startstack
0.0127694101429304 (C) numchar
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0.0356792342228939 (G) numchar
0.0401860848615752 (T) numchar
endstack
(7) startstack
0.0158395764566803 (A) numchar
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endstack
(8) startstack
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0.129784165276898 (G) numchar
endstack
(9) startstack
0.0197173066883571 (A) numchar
0.0462598349226839 (G) numchar
0.0530850564686536 (T) numchar
0.108445186785964 (C) numchar
endstack
(10) startstack
0.01490349085771 (A) numchar
0.04471047257313 (G) numchar
0.0707915815741225 (T) numchar
0.0931468178606876 (C) numchar
endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 930 3508 a(1)957 b(2)h(3)500 3784 y @beginspecial
0 @llx 0 @lly 510 @urx 141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/thetaIII2.fake.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
% * seq_4
% * seq_5
% * seq_6
% * seq_7
% * seq_8
% * seq_9
% * seq_10
% * seq_11
% * seq_12
% * seq_13
% * seq_14
% * seq_15
% * seq_16
% * seq_17
% * seq_18
% * seq_19
% * seq_20
% * seq_21
% * seq_22
% * seq_23
% * seq_24
% * seq_25
% * seq_26
% * seq_27
% * seq_28
% * seq_29
% * seq_30
% * seq_31
% * seq_32
% * seq_33
% * seq_34
% * seq_35
% * seq_36
% * seq_37
% * seq_38
% * seq_39
% * seq_40
% * seq_41
% * seq_42
% * seq_43
% * seq_44
% * seq_45
% * seq_46
% * seq_47
% * seq_48
% * seq_49
% * seq_50
% * seq_51
% * seq_52
% * seq_53
% * seq_54
% * seq_55
% * seq_56
% * seq_57
% * seq_58
% * seq_59
% * seq_60
% * seq_61
% * seq_62
% * seq_63
% * seq_64
% * seq_65
% * seq_66
% * seq_67
% * seq_68
% * seq_69
% * seq_70
% * seq_71
% * seq_72
% * seq_73
% * seq_74
% * seq_75
% * seq_76
% * seq_77
% * seq_78
% * seq_79
% * seq_80
% * seq_81
% * seq_82
% * seq_83
% * seq_84
% * seq_85
% * seq_86
% * seq_87
% * seq_88
% * seq_89
% * seq_90
% * seq_91
% * seq_92
% * seq_93
% * seq_94
% * seq_95
% * seq_96
% * seq_97
% * seq_98
% * seq_99
% * seq_100
% * seq_101
% * seq_102
% * seq_103
% * seq_104
% * seq_105
% * seq_106
% * seq_107
% * seq_108
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% * seq_110
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% * seq_113
% * seq_114
% * seq_115
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% * seq_123
% * seq_124
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% * seq_127
% * seq_128
% * seq_129
% * seq_130
% * seq_131
% * seq_132
% * seq_133
% * seq_134
% * seq_135
% * seq_136
% * seq_137
% * seq_138
% * seq_139
% * seq_140
% * seq_141
% * seq_142
% * seq_143
% * seq_144
% * seq_145
% * seq_146
% * seq_147
% * seq_148
% * seq_149
% * seq_150
% * seq_151
% * seq_152
% * seq_153
% * seq_154
% * seq_155
% * seq_156
% * seq_157
% * seq_158
% * seq_159
% * seq_160
% * seq_161
% * seq_162
% * seq_163
% * seq_164
% * seq_165
% * seq_166
% * seq_167
% * seq_168
% * seq_169
% * seq_170
% * seq_171
% * seq_172
% * seq_173
% * seq_174
% * seq_175
% * seq_176
% * seq_177
% * seq_178
% * seq_179
% * seq_180
% * seq_181
% * seq_182
% * seq_183
% * seq_184
% * seq_185
% * seq_186
% * seq_187
% * seq_188
% * seq_189
% * seq_190
% * seq_191
% * seq_192
% * seq_193
% * seq_194
% * seq_195
% * seq_196
% * seq_197
% * seq_198
% * seq_199
% * seq_200
% * seq_201
% * seq_202
% * seq_203
% * seq_204
% * seq_205
% * seq_206
% * seq_207
% * seq_208
% * seq_209
% * seq_210
% * seq_211
% * seq_212
% * seq_213
% * seq_214
% * seq_215
% * seq_216
% * seq_217
% * seq_218
% * seq_219
% * seq_220
% * seq_221
% * seq_222
% * seq_223
% * seq_224
% * seq_225
% * seq_226
% * seq_227
% * seq_228
% * seq_229
% * seq_230
% * seq_231
% * seq_232
% * seq_233
% * seq_234
% * seq_235
% * seq_236
% * seq_237
% * seq_238
% * seq_239
% * seq_240
% * seq_241
% * seq_242
% * seq_243
% * seq_244
% * seq_245
% * seq_246
% * seq_247
% * seq_248
% * seq_249
% * seq_250
% * seq_251
% * seq_252
% * seq_253
% * seq_254
% * seq_255
% * seq_256
% * seq_257
% * seq_258
% * seq_259
% * seq_260
% * seq_261
% * seq_262
% * seq_263
% * seq_264
% * seq_265
% * seq_266
% * seq_267
% * seq_268
% * seq_269
% * seq_270
% * seq_271
% * seq_272
% * seq_273
% * seq_274
% * seq_275
% * seq_276
% * seq_277
% * seq_278
% * seq_279
% * seq_280
% * seq_281
% * seq_282
% * seq_283
% * seq_284
% * seq_285
% * seq_286
% * seq_287
% * seq_288
% * seq_289
% * seq_290
% * seq_291
% * seq_292
% * seq_293
% * seq_294
% * seq_295
% * seq_296
% * seq_297
% * seq_298
% * seq_299
% * seq_300
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 10 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
(1) startstack
0.353089839822243 (A) numchar
0.738940592617684 (T) numchar
endstack
(2) startstack
0.00751388344483204 (G) numchar
0.0676249510034883 (C) numchar
0.123979076839729 (T) numchar
0.927964605436757 (A) numchar
endstack
(3) startstack
0.00602439730206541 (C) numchar
0.051207377067556 (G) numchar
0.192780713666093 (T) numchar
0.653647107274097 (A) numchar
endstack
(4) startstack
0.0148536968481936 (G) numchar
0.0445610905445809 (T) numchar
0.0594147873927745 (C) numchar
1.36654011003381 (A) numchar
endstack
(5) startstack
0.0113842842948138 (G) numchar
0.0113842842948138 (C) numchar
0.0455371371792553 (T) numchar
1.63933693845319 (A) numchar
endstack
(6) startstack
0.010801491401855 (C) numchar
0.0162022371027825 (G) numchar
0.0648089484111301 (T) numchar
1.52841103336248 (A) numchar
endstack
(7) startstack
0.264288624614433 (A) numchar
0.994228635454294 (T) numchar
endstack
(8) startstack
0.0108761280235264 (A) numchar
0.0569397290643443 (C) numchar
0.0614181347210904 (G) numchar
0.0626976791944465 (T) numchar
endstack
(9) startstack
0.0187689034682062 (C) numchar
0.0693005666518384 (G) numchar
0.0981758027567711 (A) numchar
0.246883268697174 (T) numchar
endstack
(10) startstack
0.0118248719346669 (C) numchar
0.0325183978203339 (T) numchar
0.218760130791337 (G) numchar
0.623761994553677 (A) numchar
endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 1000 w @beginspecial 0 @llx 0 @lly 510 @urx
141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/thetaI3.fake.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
% * seq_4
% * seq_5
% * seq_6
% * seq_7
% * seq_8
% * seq_9
% * seq_10
% * seq_11
% * seq_12
% * seq_13
% * seq_14
% * seq_15
% * seq_16
% * seq_17
% * seq_18
% * seq_19
% * seq_20
% * seq_21
% * seq_22
% * seq_23
% * seq_24
% * seq_25
% * seq_26
% * seq_27
% * seq_28
% * seq_29
% * seq_30
% * seq_31
% * seq_32
% * seq_33
% * seq_34
% * seq_35
% * seq_36
% * seq_37
% * seq_38
% * seq_39
% * seq_40
% * seq_41
% * seq_42
% * seq_43
% * seq_44
% * seq_45
% * seq_46
% * seq_47
% * seq_48
% * seq_49
% * seq_50
% * seq_51
% * seq_52
% * seq_53
% * seq_54
% * seq_55
% * seq_56
% * seq_57
% * seq_58
% * seq_59
% * seq_60
% * seq_61
% * seq_62
% * seq_63
% * seq_64
% * seq_65
% * seq_66
% * seq_67
% * seq_68
% * seq_69
% * seq_70
% * seq_71
% * seq_72
% * seq_73
% * seq_74
% * seq_75
% * seq_76
% * seq_77
% * seq_78
% * seq_79
% * seq_80
% * seq_81
% * seq_82
% * seq_83
% * seq_84
% * seq_85
% * seq_86
% * seq_87
% * seq_88
% * seq_89
% * seq_90
% * seq_91
% * seq_92
% * seq_93
% * seq_94
% * seq_95
% * seq_96
% * seq_97
% * seq_98
% * seq_99
% * seq_100
% * seq_101
% * seq_102
% * seq_103
% * seq_104
% * seq_105
% * seq_106
% * seq_107
% * seq_108
% * seq_109
% * seq_110
% * seq_111
% * seq_112
% * seq_113
% * seq_114
% * seq_115
% * seq_116
% * seq_117
% * seq_118
% * seq_119
% * seq_120
% * seq_121
% * seq_122
% * seq_123
% * seq_124
% * seq_125
% * seq_126
% * seq_127
% * seq_128
% * seq_129
% * seq_130
% * seq_131
% * seq_132
% * seq_133
% * seq_134
% * seq_135
% * seq_136
% * seq_137
% * seq_138
% * seq_139
% * seq_140
% * seq_141
% * seq_142
% * seq_143
% * seq_144
% * seq_145
% * seq_146
% * seq_147
% * seq_148
% * seq_149
% * seq_150
% * seq_151
% * seq_152
% * seq_153
% * seq_154
% * seq_155
% * seq_156
% * seq_157
% * seq_158
% * seq_159
% * seq_160
% * seq_161
% * seq_162
% * seq_163
% * seq_164
% * seq_165
% * seq_166
% * seq_167
% * seq_168
% * seq_169
% * seq_170
% * seq_171
% * seq_172
% * seq_173
% * seq_174
% * seq_175
% * seq_176
% * seq_177
% * seq_178
% * seq_179
% * seq_180
% * seq_181
% * seq_182
% * seq_183
% * seq_184
% * seq_185
% * seq_186
% * seq_187
% * seq_188
% * seq_189
% * seq_190
% * seq_191
% * seq_192
% * seq_193
% * seq_194
% * seq_195
% * seq_196
% * seq_197
% * seq_198
% * seq_199
% * seq_200
% * seq_201
% * seq_202
% * seq_203
% * seq_204
% * seq_205
% * seq_206
% * seq_207
% * seq_208
% * seq_209
% * seq_210
% * seq_211
% * seq_212
% * seq_213
% * seq_214
% * seq_215
% * seq_216
% * seq_217
% * seq_218
% * seq_219
% * seq_220
% * seq_221
% * seq_222
% * seq_223
% * seq_224
% * seq_225
% * seq_226
% * seq_227
% * seq_228
% * seq_229
% * seq_230
% * seq_231
% * seq_232
% * seq_233
% * seq_234
% * seq_235
% * seq_236
% * seq_237
% * seq_238
% * seq_239
% * seq_240
% * seq_241
% * seq_242
% * seq_243
% * seq_244
% * seq_245
% * seq_246
% * seq_247
% * seq_248
% * seq_249
% * seq_250
% * seq_251
% * seq_252
% * seq_253
% * seq_254
% * seq_255
% * seq_256
% * seq_257
% * seq_258
% * seq_259
% * seq_260
% * seq_261
% * seq_262
% * seq_263
% * seq_264
% * seq_265
% * seq_266
% * seq_267
% * seq_268
% * seq_269
% * seq_270
% * seq_271
% * seq_272
% * seq_273
% * seq_274
% * seq_275
% * seq_276
% * seq_277
% * seq_278
% * seq_279
% * seq_280
% * seq_281
% * seq_282
% * seq_283
% * seq_284
% * seq_285
% * seq_286
% * seq_287
% * seq_288
% * seq_289
% * seq_290
% * seq_291
% * seq_292
% * seq_293
% * seq_294
% * seq_295
% * seq_296
% * seq_297
% * seq_298
% * seq_299
% * seq_300
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 15 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
(1) startstack
0.378108953766801 (A) numchar
0.682009608196192 (T) numchar
endstack
(2) startstack
0.013254780108625 (G) numchar
0.0747087606122502 (C) numchar
0.0891685207307502 (T) numchar
0.184361941510875 (A) numchar
endstack
(3) startstack
0.0137461194554066 (G) numchar
0.0528696902131021 (A) numchar
0.116313318468825 (T) numchar
0.134289013141279 (C) numchar
endstack
(4) startstack
0.0311340852095677 (A) numchar
0.075377258928427 (T) numchar
0.0770158949920885 (G) numchar
0.308063579968354 (C) numchar
endstack
(5) startstack
0.0262812694510521 (T) numchar
0.0431763712410142 (G) numchar
0.0666417903937393 (A) numchar
0.145485598746896 (C) numchar
endstack
(6) startstack
0.0452936070165252 (T) numchar
0.0452936070165252 (G) numchar
0.11117521722238 (C) numchar
0.415877664424458 (A) numchar
endstack
(7) startstack
0.0127608096959839 (C) numchar
0.0552968420159302 (G) numchar
0.154547584095805 (T) numchar
0.202755087391744 (A) numchar
endstack
(8) startstack
0.00570203679450766 (A) numchar
0.0741264783285996 (G) numchar
1.63078252322919 (C) numchar
endstack
(9) startstack
0.0065592321492941 (A) numchar
1.96121041263894 (C) numchar
endstack
(10) startstack
0.0065592321492941 (A) numchar
1.96121041263894 (C) numchar
endstack
(11) startstack
0.0728998888575946 (T) numchar
0.214411437816455 (G) numchar
0.355922986775315 (A) numchar
endstack
(12) startstack
0.00420734490072347 (G) numchar
0.0778358806633841 (C) numchar
0.168293796028939 (T) numchar
0.380764713515474 (A) numchar
endstack
(13) startstack
0.08999031472004 (C) numchar
0.139984934008951 (A) numchar
0.769917137049231 (T) numchar
endstack
(14) startstack
0.0065592321492941 (A) numchar
1.96121041263894 (C) numchar
endstack
(15) startstack
0.00575224700906458 (A) numchar
0.0690269641087749 (G) numchar
1.65089489160153 (C) numchar
endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 1000 w @beginspecial 0 @llx 0 @lly 510 @urx
141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/thetaIII3.fake.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
% * seq_4
% * seq_5
% * seq_6
% * seq_7
% * seq_8
% * seq_9
% * seq_10
% * seq_11
% * seq_12
% * seq_13
% * seq_14
% * seq_15
% * seq_16
% * seq_17
% * seq_18
% * seq_19
% * seq_20
% * seq_21
% * seq_22
% * seq_23
% * seq_24
% * seq_25
% * seq_26
% * seq_27
% * seq_28
% * seq_29
% * seq_30
% * seq_31
% * seq_32
% * seq_33
% * seq_34
% * seq_35
% * seq_36
% * seq_37
% * seq_38
% * seq_39
% * seq_40
% * seq_41
% * seq_42
% * seq_43
% * seq_44
% * seq_45
% * seq_46
% * seq_47
% * seq_48
% * seq_49
% * seq_50
% * seq_51
% * seq_52
% * seq_53
% * seq_54
% * seq_55
% * seq_56
% * seq_57
% * seq_58
% * seq_59
% * seq_60
% * seq_61
% * seq_62
% * seq_63
% * seq_64
% * seq_65
% * seq_66
% * seq_67
% * seq_68
% * seq_69
% * seq_70
% * seq_71
% * seq_72
% * seq_73
% * seq_74
% * seq_75
% * seq_76
% * seq_77
% * seq_78
% * seq_79
% * seq_80
% * seq_81
% * seq_82
% * seq_83
% * seq_84
% * seq_85
% * seq_86
% * seq_87
% * seq_88
% * seq_89
% * seq_90
% * seq_91
% * seq_92
% * seq_93
% * seq_94
% * seq_95
% * seq_96
% * seq_97
% * seq_98
% * seq_99
% * seq_100
% * seq_101
% * seq_102
% * seq_103
% * seq_104
% * seq_105
% * seq_106
% * seq_107
% * seq_108
% * seq_109
% * seq_110
% * seq_111
% * seq_112
% * seq_113
% * seq_114
% * seq_115
% * seq_116
% * seq_117
% * seq_118
% * seq_119
% * seq_120
% * seq_121
% * seq_122
% * seq_123
% * seq_124
% * seq_125
% * seq_126
% * seq_127
% * seq_128
% * seq_129
% * seq_130
% * seq_131
% * seq_132
% * seq_133
% * seq_134
% * seq_135
% * seq_136
% * seq_137
% * seq_138
% * seq_139
% * seq_140
% * seq_141
% * seq_142
% * seq_143
% * seq_144
% * seq_145
% * seq_146
% * seq_147
% * seq_148
% * seq_149
% * seq_150
% * seq_151
% * seq_152
% * seq_153
% * seq_154
% * seq_155
% * seq_156
% * seq_157
% * seq_158
% * seq_159
% * seq_160
% * seq_161
% * seq_162
% * seq_163
% * seq_164
% * seq_165
% * seq_166
% * seq_167
% * seq_168
% * seq_169
% * seq_170
% * seq_171
% * seq_172
% * seq_173
% * seq_174
% * seq_175
% * seq_176
% * seq_177
% * seq_178
% * seq_179
% * seq_180
% * seq_181
% * seq_182
% * seq_183
% * seq_184
% * seq_185
% * seq_186
% * seq_187
% * seq_188
% * seq_189
% * seq_190
% * seq_191
% * seq_192
% * seq_193
% * seq_194
% * seq_195
% * seq_196
% * seq_197
% * seq_198
% * seq_199
% * seq_200
% * seq_201
% * seq_202
% * seq_203
% * seq_204
% * seq_205
% * seq_206
% * seq_207
% * seq_208
% * seq_209
% * seq_210
% * seq_211
% * seq_212
% * seq_213
% * seq_214
% * seq_215
% * seq_216
% * seq_217
% * seq_218
% * seq_219
% * seq_220
% * seq_221
% * seq_222
% * seq_223
% * seq_224
% * seq_225
% * seq_226
% * seq_227
% * seq_228
% * seq_229
% * seq_230
% * seq_231
% * seq_232
% * seq_233
% * seq_234
% * seq_235
% * seq_236
% * seq_237
% * seq_238
% * seq_239
% * seq_240
% * seq_241
% * seq_242
% * seq_243
% * seq_244
% * seq_245
% * seq_246
% * seq_247
% * seq_248
% * seq_249
% * seq_250
% * seq_251
% * seq_252
% * seq_253
% * seq_254
% * seq_255
% * seq_256
% * seq_257
% * seq_258
% * seq_259
% * seq_260
% * seq_261
% * seq_262
% * seq_263
% * seq_264
% * seq_265
% * seq_266
% * seq_267
% * seq_268
% * seq_269
% * seq_270
% * seq_271
% * seq_272
% * seq_273
% * seq_274
% * seq_275
% * seq_276
% * seq_277
% * seq_278
% * seq_279
% * seq_280
% * seq_281
% * seq_282
% * seq_283
% * seq_284
% * seq_285
% * seq_286
% * seq_287
% * seq_288
% * seq_289
% * seq_290
% * seq_291
% * seq_292
% * seq_293
% * seq_294
% * seq_295
% * seq_296
% * seq_297
% * seq_298
% * seq_299
% * seq_300
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 10 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
(1) startstack
0.0127376219039173 (A) numchar
0.0409819139517338 (C) numchar
0.0498428683196763 (T) numchar
0.0625804902235935 (G) numchar
endstack
(2) startstack
0.0065592321492941 (A) numchar
1.96121041263894 (C) numchar
endstack
(3) startstack
0.0065592321492941 (A) numchar
1.96121041263894 (C) numchar
endstack
(4) startstack
0.0756273745914915 (T) numchar
0.190372356730306 (A) numchar
0.516352419624666 (G) numchar
endstack
(5) startstack
0.0124929658270198 (A) numchar
0.220709062944016 (C) numchar
1.01609455393094 (G) numchar
endstack
(6) startstack
0.0338313849395402 (T) numchar
0.0338313849395402 (A) numchar
0.0968277568959255 (G) numchar
0.185489317427134 (C) numchar
endstack
(7) startstack
0.0352585444881256 (A) numchar
0.043093776596598 (T) numchar
0.131240137816912 (C) numchar
0.378049949233791 (G) numchar
endstack
(8) startstack
0.0194654954185813 (T) numchar
0.0629766028248219 (G) numchar
0.0790070108165947 (C) numchar
0.182059633620849 (A) numchar
endstack
(9) startstack
0.0163902989525562 (C) numchar
0.0389976078526338 (A) numchar
0.0406931560201396 (G) numchar
0.073473753925252 (T) numchar
endstack
(10) startstack
0.0065592321492941 (A) numchar
1.96121041263894 (C) numchar
endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 930 3803 a(4)f(5)947 b(6)450 3902 y(Figure)16
b(5:)23 b Fy(Motif)16 b(patterns)f(detected)i(by)e Fp(LOGOS)h
Fy(with)f(the)g Fp(HMDM)g Fy(local)g(model)h(in)f(the)h(re)o(gulatory)g
(re)o(gions)450 3984 y(of)j(Drosophila)h(e)n(v)o(e-skipped)g(gene.)500
4403 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury
1080 @rwi @setspecial
%%BeginDocument: figure/M4_thetaI1.fake.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
% * seq_4
% * seq_5
% * seq_6
% * seq_7
% * seq_8
% * seq_9
% * seq_10
% * seq_11
% * seq_12
% * seq_13
% * seq_14
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% * seq_16
% * seq_17
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% * seq_19
% * seq_20
% * seq_21
% * seq_22
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% * seq_24
% * seq_25
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% * seq_32
% * seq_33
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% * seq_55
% * seq_56
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% * seq_88
% * seq_89
% * seq_90
% * seq_91
% * seq_92
% * seq_93
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% * seq_95
% * seq_96
% * seq_97
% * seq_98
% * seq_99
% * seq_100
% * seq_101
% * seq_102
% * seq_103
% * seq_104
% * seq_105
% * seq_106
% * seq_107
% * seq_108
% * seq_109
% * seq_110
% * seq_111
% * seq_112
% * seq_113
% * seq_114
% * seq_115
% * seq_116
% * seq_117
% * seq_118
% * seq_119
% * seq_120
% * seq_121
% * seq_122
% * seq_123
% * seq_124
% * seq_125
% * seq_126
% * seq_127
% * seq_128
% * seq_129
% * seq_130
% * seq_131
% * seq_132
% * seq_133
% * seq_134
% * seq_135
% * seq_136
% * seq_137
% * seq_138
% * seq_139
% * seq_140
% * seq_141
% * seq_142
% * seq_143
% * seq_144
% * seq_145
% * seq_146
% * seq_147
% * seq_148
% * seq_149
% * seq_150
% * seq_151
% * seq_152
% * seq_153
% * seq_154
% * seq_155
% * seq_156
% * seq_157
% * seq_158
% * seq_159
% * seq_160
% * seq_161
% * seq_162
% * seq_163
% * seq_164
% * seq_165
% * seq_166
% * seq_167
% * seq_168
% * seq_169
% * seq_170
% * seq_171
% * seq_172
% * seq_173
% * seq_174
% * seq_175
% * seq_176
% * seq_177
% * seq_178
% * seq_179
% * seq_180
% * seq_181
% * seq_182
% * seq_183
% * seq_184
% * seq_185
% * seq_186
% * seq_187
% * seq_188
% * seq_189
% * seq_190
% * seq_191
% * seq_192
% * seq_193
% * seq_194
% * seq_195
% * seq_196
% * seq_197
% * seq_198
% * seq_199
% * seq_200
% * seq_201
% * seq_202
% * seq_203
% * seq_204
% * seq_205
% * seq_206
% * seq_207
% * seq_208
% * seq_209
% * seq_210
% * seq_211
% * seq_212
% * seq_213
% * seq_214
% * seq_215
% * seq_216
% * seq_217
% * seq_218
% * seq_219
% * seq_220
% * seq_221
% * seq_222
% * seq_223
% * seq_224
% * seq_225
% * seq_226
% * seq_227
% * seq_228
% * seq_229
% * seq_230
% * seq_231
% * seq_232
% * seq_233
% * seq_234
% * seq_235
% * seq_236
% * seq_237
% * seq_238
% * seq_239
% * seq_240
% * seq_241
% * seq_242
% * seq_243
% * seq_244
% * seq_245
% * seq_246
% * seq_247
% * seq_248
% * seq_249
% * seq_250
% * seq_251
% * seq_252
% * seq_253
% * seq_254
% * seq_255
% * seq_256
% * seq_257
% * seq_258
% * seq_259
% * seq_260
% * seq_261
% * seq_262
% * seq_263
% * seq_264
% * seq_265
% * seq_266
% * seq_267
% * seq_268
% * seq_269
% * seq_270
% * seq_271
% * seq_272
% * seq_273
% * seq_274
% * seq_275
% * seq_276
% * seq_277
% * seq_278
% * seq_279
% * seq_280
% * seq_281
% * seq_282
% * seq_283
% * seq_284
% * seq_285
% * seq_286
% * seq_287
% * seq_288
% * seq_289
% * seq_290
% * seq_291
% * seq_292
% * seq_293
% * seq_294
% * seq_295
% * seq_296
% * seq_297
% * seq_298
% * seq_299
% * seq_300
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 15 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
(1) startstack
0.00735803708325766 (A) numchar
0.0784857288880817 (G) numchar
0.116502253818246 (C) numchar
0.165555834373297 (T) numchar
endstack
(2) startstack
0.0119366338788029 (C) numchar
0.0198943897980048 (G) numchar
0.179049508182043 (A) numchar
0.982782856021438 (T) numchar
endstack
(3) startstack
0.0135348302052027 (C) numchar
0.0225580503420045 (A) numchar
0.126325081915225 (G) numchar
1.19106505805784 (T) numchar
endstack
(4) startstack
0.0178541050462744 (C) numchar
0.0446352626156859 (G) numchar
0.0892705252313718 (A) numchar
1.18729798557724 (T) numchar
endstack
(5) startstack
0.0087842109600469 (A) numchar
0.039528949320211 (C) numchar
0.261330276061395 (G) numchar
0.349172385661864 (T) numchar
endstack
(6) startstack
0.0208914075041675 (A) numchar
0.0515321385102798 (G) numchar
0.118384642523616 (T) numchar
0.227019961545287 (C) numchar
endstack
(7) startstack
0.0430788328697705 (A) numchar
0.0553870708325621 (C) numchar
0.0753879575220983 (T) numchar
0.287705062380253 (G) numchar
endstack
(8) startstack
0.014427976084787 (G) numchar
0.0396769342331643 (A) numchar
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0.869285559108418 (C) numchar
endstack
(9) startstack
0.00956942644656034 (A) numchar
0.0727276409938586 (G) numchar
0.149283052566341 (T) numchar
0.34258546678686 (C) numchar
endstack
(10) startstack
0.0130302726924521 (T) numchar
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0.703634725392415 (G) numchar
endstack
(11) startstack
0.0146180246436218 (T) numchar
0.0310633023676963 (C) numchar
0.0356314350688281 (G) numchar
0.0557312189538081 (A) numchar
endstack
(12) startstack
0.0375790886304189 (T) numchar
0.0375790886304189 (A) numchar
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0.189034203413623 (G) numchar
endstack
(13) startstack
0.0100088573715953 (G) numchar
0.0250221434289883 (A) numchar
0.302767935490759 (T) numchar
0.412865366578307 (C) numchar
endstack
(14) startstack
0.0280069630174335 (A) numchar
0.0541467951670381 (C) numchar
0.123230637276707 (G) numchar
0.354754864887491 (T) numchar
endstack
(15) startstack
0.0262527360196684 (G) numchar
0.0288780096216352 (T) numchar
0.0953849408714618 (C) numchar
0.112011673683919 (A) numchar
endstack
EndLine
EndLogo
%%EOF
%%EndDocument
@endspecial 1000 w @beginspecial 0 @llx 0 @lly 510 @urx
141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/M4_thetaII1.fake.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
% * seq_4
% * seq_5
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% * seq_228
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% * seq_237
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% * seq_239
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% * seq_241
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% * seq_243
% * seq_244
% * seq_245
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% * seq_247
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% * seq_249
% * seq_250
% * seq_251
% * seq_252
% * seq_253
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% * seq_255
% * seq_256
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% * seq_260
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% * seq_262
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% * seq_264
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% * seq_268
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% * seq_270
% * seq_271
% * seq_272
% * seq_273
% * seq_274
% * seq_275
% * seq_276
% * seq_277
% * seq_278
% * seq_279
% * seq_280
% * seq_281
% * seq_282
% * seq_283
% * seq_284
% * seq_285
% * seq_286
% * seq_287
% * seq_288
% * seq_289
% * seq_290
% * seq_291
% * seq_292
% * seq_293
% * seq_294
% * seq_295
% * seq_296
% * seq_297
% * seq_298
% * seq_299
% * seq_300
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 20 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW rlineto
stroke
newpath
0 height moveto
0 height rmoveto
currentpoint translate
ShowIbar
newpath
0 0 moveto
0 heightDRAW neg rlineto
currentpoint translate
stroke
grestore
} bind def
/ShowIbar { % make a horizontal bar
gsave
newpath
charWidth4 neg 0 moveto
charWidth4 0 lineto
stroke
grestore
} bind def
/ShowLeftEnd {
gsave
SetStringFont
leftEndDeltaX leftEndDeltaY moveto
showEnds (d) eq {(5) show ShowPrime} if
showEnds (p) eq {(N) show} if
grestore
} bind def
/ShowRightEnd {
gsave
SetStringFont
rightEndDeltaX rightEndDeltaY moveto
showEnds (d) eq {(3) show ShowPrime} if
showEnds (p) eq {(C) show} if
grestore
} bind def
/ShowPrime {
gsave
SetPrimeFont
(\242) show
grestore
} bind def
/SetColor{ % SetColor
dup colorDict exch known {
colorDict exch get aload pop setrgbcolor
} {
pop
defaultColor aload pop setrgbcolor
} ifelse
} bind def
% define fonts
/SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def
/SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def
/SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def
/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def
/SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def
/SetNumberFont {
/Helvetica-Bold findfont
numberFontsize
scalefont
setfont
} bind def
%Take a single character and return the bounding box
/CharBox { % CharBox
gsave
newpath
0 0 moveto
% take the character off the stack and use it here:
true charpath
flattenpath
pathbbox % compute bounding box of 1 pt. char => lx ly ux uy
% the path is here, but toss it away ...
grestore
} bind def
% The height of a characters bounding box
/CharBoxHeight { % CharBoxHeight
CharBox
exch pop sub neg exch pop
} bind def
% The width of a characters bounding box
/CharBoxWidth { % CharBoxHeight
CharBox
pop exch pop sub neg
} bind def
% Deprecated names
/startstack {StartStack} bind def
/endstack {EndStack} bind def
/makenumber {MakeNumber} bind def
/numchar { MakeSymbol } bind def
%%EndProlog
%%Page: 1 1
StartLogo
StartLine % line number 1
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%%EOF
%%EndDocument
@endspecial 1000 w @beginspecial 0 @llx 0 @lly 510 @urx
141 @ury 1080 @rwi @setspecial
%%BeginDocument: figure/M4_thetaIII1.fake.fasta.eps
%!PS-Adobe-3.0 EPSF-3.0
%%Title: Sequence Logo:
%%Creator: seqlogo (1.0)
%%CreationDate:
%%BoundingBox: 0 0 510 141
%%Pages: 0
%%DocumentFonts:
%%EndComments
% * seq_1
% * seq_2
% * seq_3
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% * seq_283
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% * seq_287
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% * seq_290
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% * seq_294
% * seq_295
% * seq_296
% * seq_297
% * seq_298
% * seq_299
% * seq_300
% * NUCLEOTIDE ALIGNMENT
% ---- CONSTANTS ----
/cmfactor 72 2.54 div def % defines points -> cm conversion
/cm {cmfactor mul} bind def % defines centimeters
% ---- VARIABLES ----
/black [0 0 0] def
/red [0.8 0 0] def
/green [0 0.8 0] def
/blue [0 0 0.8] def
/yellow [1 0.71 .0] def
/purple [0.8 0 0.8] def
/orange [1 0.7 0] def
/logoWidth 18 cm def
/logoHeight 5 cm def
/logoTitle () def
/yaxis true def
/yaxisLabel (bits) def
/yaxisBits 2 def % bits
/xaxis true def
/xaxisLabel ( ) def
/showEnds (d) def % d: DNA, p: PROTEIN, -: none
/showFineprint true def
/fineprint () def
/charsPerLine 10 def
/logoLines 1 def
/showingBox (n) def %n s f
/shrinking false def
/shrink 1 def
/outline false def
/IbeamFraction 1 def
/IbeamGray 0.75 def
/IbeamLineWidth 0.5 def
/fontsize 12 def
/titleFontsize 14 def
/smallFontsize 6 def
/defaultColor black def
% Standard DNA/RNA color scheme
/colorDict <<
(G) orange
(T) red
(C) blue
(A) green
(U) red
>> def
% Standard DNA/RNA color scheme
% /colorDict <<
% (G) orange
% (T) red
% (C) blue
% (A) green
% (U) red
% >> def
% Standard Amino Acid colors
%/colorDict <<
% (G) green
% (S) green
% (T) green
% (Y) green
% (C) green
% (N) purple
% (Q) purple
% (K) blue
% (R) blue
% (H) blue
% (D) red
% (E) red
% (P) black
% (A) black
% (W) black
% (F) black
% (L) black
% (I) black
% (M) black
% (V) black
%>> def
% ---- DERIVED PARAMETERS ----
/leftMargin fontsize 2.5 mul def
/bottomMargin
fontsize 0.75 mul
% Add extra room for axis
xaxis {fontsize 1.75 mul add } if
xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse
def
/topMargin
logoTitle () eq { 10 }{titleFontsize 4 add} ifelse
def
/rightMargin
%Add extra room if showing ends
showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse
def
/yaxisHeight
logoHeight
bottomMargin sub
topMargin sub
def
/ticWidth fontsize 2 div def
/pointsPerBit yaxisHeight yaxisBits div def
/isBoxed
showingBox (s) eq
showingBox (f) eq or {
true
} {
false
} ifelse
def
/stackMargin 1 def
% Do not add space aroung characters if characters are boxed
/charRightMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charTopMargin
isBoxed { 0.0 } {stackMargin} ifelse
def
/charWidth
logoWidth
leftMargin sub
rightMargin sub
charsPerLine div
charRightMargin sub
def
/charWidth4 charWidth 4 div def
/charWidth2 charWidth 2 div def
/stackWidth
charWidth charRightMargin add
def
/numberFontsize
fontsize charWidth lt {fontsize}{charWidth} ifelse
def
% movements to place 5'/N and 3'/C symbols
/leftEndDeltaX fontsize neg def
/leftEndDeltaY fontsize 1.5 mul neg def
/rightEndDeltaX fontsize 0.25 mul def
/rightEndDeltaY leftEndDeltaY def
% Outline width is proporional to charWidth,
% but no less that 1 point
/outlinewidth
charWidth 32 div dup 1 gt {}{pop 1} ifelse
def
% ---- PROCEDURES ----
/StartLogo {
% Save state
save
gsave
% Print Logo Title, top center
gsave
SetTitleFont
logoWidth 2 div
logoTitle
stringwidth pop 2 div sub
logoHeight logoLines mul
titleFontsize sub
moveto
logoTitle
show
grestore
% Print X-axis label, bottom center
gsave
SetStringFont
logoWidth 2 div
xaxisLabel stringwidth pop 2 div sub
fontsize 3 div
moveto
xaxisLabel
show
grestore
% Show Fine Print
showFineprint {
gsave
SetSmallFont
logoWidth
fineprint stringwidth pop sub
smallFontsize sub
smallFontsize 3 div
moveto
fineprint show
grestore
} if
% Move to lower left corner of last line, first stack
leftMargin bottomMargin translate
% Move above first line ready for StartLine
0 logoLines logoHeight mul translate
SetLogoFont
} bind def
/EndLogo {
grestore
showpage
restore
} bind def
/StartLine{
% move down to the bottom of the line:
0 logoHeight neg translate
gsave
yaxis { MakeYaxis } if
xaxis { ShowLeftEnd } if
} bind def
/EndLine{
xaxis { ShowRightEnd } if
grestore
} bind def
/MakeYaxis {
gsave
stackMargin neg 0 translate
ShowYaxisBar
ShowYaxisLabel
grestore
} bind def
/ShowYaxisBar {
gsave
SetStringFont
/str 10 string def % string to hold number
/smallgap stackMargin 2 div def
% Draw first tic and bar
gsave
ticWidth neg 0 moveto
ticWidth 0 rlineto
0 yaxisHeight rlineto
stroke
grestore
% Draw the tics
% initial increment limit proc for
0 1 yaxisBits abs cvi
{/loopnumber exch def
% convert the number coming from the loop to a string
% and find its width
loopnumber 10 str cvrs
/stringnumber exch def % string representing the number
stringnumber stringwidth pop
/numberwidth exch def % width of number to show
/halfnumberheight
stringnumber CharBoxHeight 2 div
def
numberwidth % move back width of number
neg loopnumber pointsPerBit mul % shift on y axis
halfnumberheight sub % down half the digit
moveto % move back the width of the string
ticWidth neg smallgap sub % Move back a bit more
0 rmoveto % move back the width of the tic
stringnumber show
smallgap 0 rmoveto % Make a small gap
% now show the tic mark
0 halfnumberheight rmoveto % shift up again
ticWidth 0 rlineto
stroke
} for
grestore
} bind def
/ShowYaxisLabel {
gsave
SetStringFont
ticWidth neg 2.75 mul
yaxisHeight
yaxisLabel stringwidth pop
sub 2 div
translate
90 rotate
0 0 moveto
yaxisLabel show
grestore
} bind def
/StartStack { % startstack
xaxis {MakeNumber}{pop} ifelse
gsave
} bind def
/EndStack {
grestore
stackWidth 0 translate
} bind def
% Draw a character whose height is proportional to symbol bits
/MakeSymbol{ % charbits character MakeSymbol
gsave
/char exch def
/bits exch def
/bitsHeight
bits pointsPerBit mul
def
/charHeight
bitsHeight charTopMargin sub
dup
0.0 gt {}{pop 0.0} ifelse % if neg replace with zero
def
charHeight 0.0 gt {
char SetColor
charWidth charHeight char ShowChar
showingBox (s) eq { % Unfilled box
0 0 charWidth charHeight false ShowBox
} if
showingBox (f) eq { % Filled box
0 0 charWidth charHeight true ShowBox
} if
} if
grestore
0 bitsHeight translate
} bind def
/ShowChar { % ShowChar
gsave
/tc exch def % The character
/ysize exch def % the y size of the character
/xsize exch def % the x size of the character
/xmulfactor 1 def
/ymulfactor 1 def
% if ysize is negative, make everything upside down!
ysize 0 lt {
% put ysize normal in this orientation
/ysize ysize abs def
xsize ysize translate
180 rotate
} if
shrinking {
xsize 1 shrink sub 2 div mul
ysize 1 shrink sub 2 div mul translate
shrink shrink scale
} if
% Calculate the font scaling factors
% Loop twice to catch small correction due to first scaling
2 {
gsave
xmulfactor ymulfactor scale
ysize % desired size of character in points
tc CharBoxHeight
dup 0.0 ne {
div % factor by which to scale up the character
/ymulfactor exch def
} % end if
{pop pop}
ifelse
xsize % desired size of character in points
tc CharBoxWidth
dup 0.0 ne {
div % factor by which to scale up the character
/xmulfactor exch def
} % end if
{pop pop}
ifelse
grestore
} repeat
% Adjust horizontal position if the symbol is an I
tc (I) eq {
charWidth 2 div % half of requested character width
tc CharBoxWidth 2 div % half of the actual character
sub 0 translate
% Avoid x scaling for I
/xmulfactor 1 def
} if
% ---- Finally, draw the character
newpath
xmulfactor ymulfactor scale
% Move lower left corner of character to start point
tc CharBox pop pop % llx lly : Lower left corner
exch neg exch neg
moveto
outline { % outline characters:
outlinewidth setlinewidth
tc true charpath
gsave 1 setgray fill grestore
clip stroke
} { % regular characters
tc show
} ifelse
grestore
} bind def
/ShowBox { % x1 y1 x2 y2 filled ShowBox
gsave
/filled exch def
/y2 exch def
/x2 exch def
/y1 exch def
/x1 exch def
newpath
x1 y1 moveto
x2 y1 lineto
x2 y2 lineto
x1 y2 lineto
closepath
clip
filled {
fill
}{
0 setgray stroke
} ifelse
grestore
} bind def
/MakeNumber { % number MakeNumber
gsave
SetNumberFont
stackWidth 0 translate
90 rotate % rotate so the number fits
dup stringwidth pop % find the length of the number
neg % prepare for move
stackMargin sub % Move back a bit
charWidth (0) CharBoxHeight % height of numbers
sub 2 div %
moveto % move back to provide space
show
grestore
} bind def
/Ibeam{ % heightInBits Ibeam
gsave
% Make an Ibeam of twice the given height in bits
/height exch pointsPerBit mul def
/heightDRAW height IbeamFraction mul def
IbeamLineWidth setlinewidth
IbeamGray setgray
charWidth2 height neg translate
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b(.)23 b(Nib)o(u,)h(B.)f(D.)g(Pfeif)n(fer)m(,)g(P)-8
b(.)22 b(T)-6 b(omancak,)25 b(S.)e(E.)f(Celnik)o(er)m(,)j(M.)e(Le)n
(vine,)i(G.)d(M.)i(Rubin,)616 3220 y(and)16 b(M.)g(B.)f(Eisen.)k
(Exploiting)d(transcription)h(f)o(actor)f(binding)g(site)g(clustering)g
(to)f(identify)h(cis-re)o(gulatory)616 3302 y(modules)23
b(in)m(v)o(olv)o(ed)g(in)f(pattern)g(formation)g(in)g(the)h(drosophila)
g(genome.)38 b Fq(Pr)m(oc.)21 b(Natl.)h(Acad.)g(Sci.)f(USA)p
Fy(,)616 3384 y(99:757\226762,)g(2002.)487 3498 y([4])42
b(E.)18 b(H.)g(Da)o(vidson.)28 b Fq(Genomic)19 b(Re)m(gulatory)h
(Systems)p Fy(.)27 b(Academic)20 b(Press,)e(2001.)487
3611 y([5])42 b(Mik)o(e)20 b(Eisen.)27 b(Structural)18
b(properties)i(of)f(transcription)g(f)o(actor)o(-DN)m(A)g(interactions)
g(and)h(the)f(inference)h(of)616 3693 y(sequence)h(speci\002city)-5
b(.)26 b(manuscript)20 b(in)f(preparation.)487 3807 y([6])42
b(D.)21 b(GuhaThakurta)h(and)g(G.)e(D.)h(Stormo.)34 b(Identifying)21
b(tar)o(get)g(sites)g(for)g(cooperati)n(v)o(ely)i(binding)f(f)o
(actors.)616 3889 y Fq(Bioinform.)p Fy(,)c(17:608\226621,)j(2001.)487
4003 y([7])42 b(D.)17 b(Heck)o(erman,)i(D.)e(Geiger)m(,)h(and)g(D.)g
(M.)f(Chik)o(ering.)25 b(Learning)19 b(Bayesian)f(netw)o(orks:)24
b(the)17 b(combination)616 4085 y(of)i(kno)n(wledge)i(and)e(statistics)
f(data.)27 b Fq(Mac)o(hine)20 b(Learning)p Fy(,)g(20:197\226243,)h
(1995.)487 4198 y([8])42 b(J.)21 b(V)-8 b(an)21 b(Helden,)h(A.)f(Rios,)
h(and)g(J.)f(Collado-V)l(ides.)34 b(Disco)o(v)o(ering)23
b(re)o(gulatory)f(elements)f(in)h(non-coding)616 4281
y(sequences)f(by)e(analysis)g(of)g(spaced)h(dyads.)28
b Fq(Nucleic)19 b(Acids)g(Res.)p Fy(,)f(28:1808\2261818,)k(2000.)487
4394 y([9])42 b(G.)18 b(Z.)f(Hertz)h(and)h(G.)e(D.)h(Stormo.)25
b(Identifying)19 b(dna)g(and)f(protein)h(patterns)g(with)e
(statistically)h(signi\002cant)616 4476 y(alignments)i(of)f(multiple)f
(sequences.)29 b Fq(Bioinform.)p Fy(,)18 b(15:563\226577,)j(1999.)450
4590 y([10])42 b(M.)25 b(I.)g(Jordan,)j(Z.)d(Ghahramani,)j(T)-6
b(.)25 b(S.)g(Jaakk)o(ola,)j(and)e(L.)f(K.)g(Saul.)48
b(An)25 b(introduction)i(to)e(v)n(ariational)616 4672
y(methods)i(for)g(graphical)g(models.)51 b(In)27 b(M.)f(I.)g(Jordan,)j
(editor)m(,)f Fq(Learning)f(in)f(Gr)o(aphical)h(Models)p
Fy(.)g(MIT)616 4754 y(Press,)18 b(Cambridge,)h(1999.)450
4868 y([11])42 b(K.)18 b(K)n(echris,)g(E.)f(v)n(an)i(Zwet,)f(P)-8
b(.)16 b(Bick)o(el,)j(and)f(M.)g(Eisen.)26 b(Detecting)18
b(DN)m(A)g(re)o(gulatory)h(motifs)f(by)h(incopo-)616
4950 y(rating)g(position-speci\002c)h(base)f(conserv)n(ation.)29
b Fq(submitted)p Fy(,)19 b(2003.)p eop
%%Page: 15 15
15 14 bop 450 83 a Fy([12])42 b(C.)18 b(La)o(wrence)g(and)h(A.)f
(Reilly)-5 b(.)25 b(An)18 b(e)o(xpectation)i(maximization)f(\(EM\))e
(algorithm)i(for)f(the)h(identi\002cation)616 165 y(and)k
(characterization)h(of)e(common)i(sites)f(in)f(unaligned)i(biopolymer)g
(sequences.)41 b Fq(Pr)m(oteins)p Fy(,)22 b(7:41\22651,)616
247 y(1990.)450 363 y([13])42 b(C.E.)23 b(La)o(wrence,)i(S.F)-6
b(.)22 b(Altschul,)j(M.S.)e(Boguski,)j(J.S.)c(Liu,)j(A.F)-6
b(.)22 b(Neuw)o(ald,)k(and)f(J.C.)e(W)-6 b(ootton.)43
b(De-)616 445 y(tecting)28 b(subtle)g(sequence)i(signals:)41
b(a)28 b(gibbs)g(sampling)h(strate)o(gy)f(for)f(multiple)h(alignment.)
56 b Fq(Science)p Fy(,)616 527 y(262:208\226214,)22 b(1993.)450
643 y([14])42 b(J.)25 b(Liu,)h(X.)f(Liu,)h(and)g(D.L.)f(Brutlag.)47
b(Bioprospector:)37 b(Disco)o(v)o(ering)27 b(conserv)o(ed)g(DN)m(A)e
(motifs)g(in)g(up-)616 725 y(stream)19 b(re)o(gulatory)h(re)o(gions)f
(of)g(co-e)o(xpressed)i(genes.)27 b(In)19 b Fq(Pr)m(oc.of)g(PSB)p
Fy(,)f(2001.)450 840 y([15])42 b(J.S.)28 b(Liu,)k(A.F)-6
b(.)28 b(Neuw)o(ald,)33 b(and)e(C.E.)d(La)o(wrence.)62
b(Bayesian)30 b(models)g(for)g(multiple)f(local)h(sequence)616
922 y(alignment)20 b(and)f(Gibbs)g(sampling)h(strate)o(gies.)27
b Fq(J)n(.)18 b(Amer)-8 b(.)18 b(Statistical)h(Assoc)p
Fy(,)g(90:1156\2261169,)j(1995.)450 1038 y([16])42 b(L.)29
b(A.)g(Pennacchio)j(and)e(E.)f(M.)h(Rubin.)63 b(Genomic)31
b(strate)o(gies)e(to)h(identify)g(mammalian)h(re)o(gulatory)616
1120 y(sequences.)d Fq(Natur)m(e)20 b(Re)o(vie)o(ws)e(Genetics)p
Fy(,)h(2\(2\):100\226109,)i(2001.)450 1235 y([17])42
b(T)-6 b(.)25 b(D.)h(Schneider)g(and)h(R.)e(M.)h(Stephens.)50
b(Sequence)27 b(logos:)38 b(A)25 b(ne)n(w)h(w)o(ay)h(to)f(display)g
(consensus)i(se-)616 1318 y(quences.)g Fq(Nucl.)19 b(Acids)f(Res.)p
Fy(,)g(18:6097\2266100,)k(1990.)450 1433 y([18])42 b(L.)18
b(Stryer)l(.)26 b Fq(Bioc)o(hemistry)19 b(\(4th.)g(edition\))p
Fy(.)27 b(W)-7 b(.)18 b(H.)g(Freeman)h(and)h(Compan)o(y)-5
b(,)20 b(1995.)450 1548 y([19])42 b(E.)16 b(P)-8 b(.)16
b(Xing,)i(M.)f(I.)g(Jordan,)h(R.)f(M.)g(Karp,)h(and)g(S.)e(Russell.)23
b(A)17 b(hierarchical)h(Bayesian)g(Mark)o(o)o(vian)h(model)616
1631 y(for)25 b(motifs)f(in)h(biopolymer)g(sequences.)47
b(In)25 b Fq(Pr)m(oc.)f(of)h(Advances)g(in)g(Neur)o(al)g(Information)g
(Pr)m(ocessing)616 1713 y(Systems)19 b(15)p Fy(,)g(2002.)450
1828 y([20])42 b(E.)15 b(P)-8 b(.)16 b(Xing)g(and)h(R.)f(M.)g(Karp.)22
b(LOGOS:)15 b(A)h(hierarchical)h(Bayesian)g(Mark)o(o)o(vian)h(motif)e
(model)h(capturing)616 1910 y(local)i(site-dependencies)i(and)e(global)
h(motif)e(distrib)o(utions.)27 b(In)19 b Fq(UC)g(T)-7
b(ec)o(hnical)19 b(Report)p Fy(,)g(2003.)p eop
%%Trailer
end
userdict /end-hook known{end-hook}if
%%EOF