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
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).
#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.
-- gilbertd at bio.indiana.edu