Software to graph sequence alignment

eugene veklerov veklerov at spindle.ee.lbl.gov
Tue Mar 9 13:51:33 EST 1993


A few days ago, I mentioned our program that presents XDAP's output
of sequence assembly in a graphical form.  I've received several
inquiries about the program.  Here is what it does.

It reads a file like this:

 Total contig length      3744.  Average length     3744.0
 Total characters in gel readings     11253.
 Average gel characters per consensus character       3.01
 Number of gel readings   32 Number of contigs    1
 
 CONTIG      LINE  LENGTH               ENDS
                                     LEFT   RIGHT
               49    3744              15       6
 NAME      NUMBER POSITION LENGTH     NEIGHBOURS
                                     LEFT   RIGHT
 54=           15        1   -154       0       1
 6=             1        1    350      15      31
 c131=         31        5   -377       1      16
 55=           16      150    306      31      14
 53=           14      260   -387      16      12
 42=           12      399   -439      14      30
 ................................................

that is familiar to everyone using XDAP and plots the segments as lines
with right or left arrows.  By pressing one of the buttons, the user
can display all gaps in both directions.

I'd be happy to send the program to everyone who wants to use it for free.
However, when I wrote the program, I had our users in mind.  Hence any
other user may have to make a couple of minor modifications.

Specifically, our biologists store groups of ABI files for adjacent
segments in parallel directories.  Then the process all the files in
each directory and write the output like the one above in the same
directory and name the output 'text'.  My program has a menu button
that displays all files named 'text' in the parallel directories.
You may have to change this feature depending on the organization of
your directories.

The program runs on the Sun.  It is written in C and X.  It is described
in the book of abstracts of the recent DOE Contractor-Grantee Workshop
in Santa Fe, page 46.

The program has evolved since it was originally written.  Hence, it
does not look straight-forward.  This means that I should explain its
organization to anyone who will attempt to adapt it to his/her environment.
I can provide some guidance on a VERY limited basis.

Eugene Veklerov
Lawrence Berkeley Laboratory




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