The materials in the "Assigned Reading" column are directly
related to the topics covered in class. Readings under
"Additional Topics" are strictly optional and will not be covered
on the exams.
In some cases, the same material is covered in
more than one textbook. You have the choice of selecting the text
that presents a treatment of the material most to your liking. It
is your responsibility to make sure that you understand the
material covered in class and you may read as many or as few of
these texts needed to achieve that goal.
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1. | Aug. 26 |
Introduction to computational biology and genomics:
part 1
, part 2
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Review biology and algorithms background | |
2. | Aug. 28 | Global pairwise sequence alignment Lecture notes | Global
sequence alignment notes, courtesy Dr. M. Singh, Princeton University |
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3. | Sep. 2 |
Global and semiglobal alignment
Lecture notes |
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4. | Sep. 4 |
Semiglobal and local pairwise alignment Lecture notes |
courtesy Dr. M. Singh, Princeton University |
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5. | Sep. 9 |
Local Pairwise alignment,
examples Literature assignments, Lecture notes |
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6. | Sep. 11 |
Intro to Markov chains
Lecture notes |
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7. | Sep. 16 |
Markov chains, continued.
Lecture notes Roig |
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8. | Sep. 18 |
Markov models of sequence evolution,
the Jukes Cantor model. Lecture notes |
Durbin, et al: 8.2, pp. 193 - 197 (electronic reserves) | |
9. | Sep. 23 |
Markov models of sequence evolution, cont'd. |
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10. | Sep. 25 |
Markov models of amino acid replacement
PAM substitution matrices New improved lecture notes PAM250, PAM30 |
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11. | Sep. 30 |
Substitution matrices
BLOSUM matrices BLOSUM45, BLOSUM80 |
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12. | Oct. 2 |
BLOSUM matrices
Lecture notes |
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13. | Oct. 7 |
Data base searching, BLAST statistics Lecture notes |
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14. | Oct. 9 |
The 1990 and 1997 BLAST heuristics Lecture notes |
Gapped BLAST
: a new generation of protein database
search programs. Altschul et al., Nucl. Acids Res. (1997)
25 (17). Assigned reading: pp. 3389-3394 only. |
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15. | Oct. 14 |
In-class exam This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Study guide |
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16. | Oct. 16 |
Gapped BLAST lecture notes |
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17. | Oct. 21 |
Class is canceled |
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18. | Oct. 23 |
BLAST statistics and information content
Lecture notes, slides |
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19. | Oct. 28 |
Local multiple alignment, PSSM's slides, PSSM example, with and without pseudocounts |
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20. | Oct. 30 |
Local multiple alignment Discovery: The Gibbs Sampler Lecture notes |
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21. | Nov. 4 |
Hidden Markov Models lecture notes |
Hidden Markov Models in Computational
Biology: Applications to Protein
Modeling, Krogh et al., JMB 235, pp 1501--1531,(1994). (electronic reserve). |
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22. | Nov. 6 |
Hidden Markov Models, cont'd lecture notes |
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23. | Nov. 11 |
HMMs, the Forward and Viterbi algorithms lecture notes Forward example, Viterbi example |
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24. | Nov. 13 |
Motif recognition with HMMs
lecture notes |
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25. | Nov. 18 |
Hidden Markov Models Parameter estimation, topology lecture notes |
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26. | Nov. 20 |
In-class exam This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Study guide |
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27. | Nov. 25 |
Class is
cancelled
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Nov. 27 | No class (Thanksgiving Holiday) | |||
28. | Dec. 2 |
Profile HMM's. Global alignment with HMM's.
lecture notes
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29. | Dec. 4 |
Global Multiple Sequence Alignment (MSA),
lecture notes
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FINAL | Dec 11
1pm - 4pm |
Final exam, Porter Hall A18B Study guide This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. |