gene structure visualisation software needed

Don Gilbert gilbertd at bio.indiana.edu
Tue May 30 14:05:25 EST 2000


Jeroen & others,

I've packaged a sample set of gnomap software and data if you
or others wish to give it a try.  Find at
http://iubio.bio.indiana.edu/soft/molbio/java/apps/gnomap/
See sample data in the testd/ and output in the pix/ folders
here.  The gnomap.jar and readseq.jar program files are needed
along with other bits there.

The instructions are terse as yet.  It does run as a command line
program (using Java jre).  You need to prepare data in its format,
which isn't too odd - mainly feature name, gene name/label, and
map range (in bases using GenBank/EMBL feature table syntax).
E.g.,
#Feature gene    map     range
gene    cTel7X.1        -       complement(709..1328)
mRNA	cTel7X.1	-	complement(join(709..822,1182..1328))
tandem_repeat   -       -       2382..2645

let me know if you have any success with it.

- Don

--
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at bio.indiana.edu







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