* stem finder

This is a display tool to see some possible stack region of RNA. It is written with
 C-language,Xlib and OSF/Motif. This program  works on a UNIX workstation with 
 OSF/Motif.

* How to Install

  1.Please copy the program files(./src/*) into some directory on the UNIX file systemes.

  2.Please do "make".


* How to use.

  % ste [filename]


  - About Menu

    .File

       Open    Select data file from FileSelectionDialog.  
               Files with extention ".aed" are listed in the file list.
               About datafile format, please referr sample files.

       Quit    Quit the program.

    .Pair

       Show Pairs
               Open new window and shows possible stack regions using circle.
               Explanation on the scales and buttons on this window ,
               please referr "Buttons, Scales and List" section below.

    .Select

       View Mode
               default mode. Only showing alignments.

       Select Mode
               You can select sequences by clicking left mouse button on them.

       Select Ok
               Open new window and shows possible stack region within the selected 
               sequences.
               Explanation on the scales and buttons on this window ,
               please referr "Buttons, Scales and List" section below.
               
       Select Cancel
               Cancel the selection of sequences.


  - Buttons , Scales and List
 
      .Close   close window.

      .scale1: percent
              "percent" scale  indicates the consensus percent  in the alignment 
               column (i.e. if certain column of alignment is consist of only 'A',
               it is 100% consensus) .
               If alignment is consist of one sequence, percent is set to 100 
               automatically.

      .scale2: consecutive
              "consecutive" scale indicates threshold of how many consecutive 
               complementary nucleic acid pairs to be considerd as "stack region".
         
      .list
               Shows column number of nucleic acid pair.
               You can select certain pairs by clicking ( mouse left button ) on pairs.

          ok       Indicates the pair column in the alignment.

          cancel   Cancel the selection of pairs.

