gene structure visualisation software needed

Jeroen Raes jerae at gengenp.rug.ac.be
Tue May 30 04:22:37 EST 2000


Dear Don,

thanks again for the quick reply... I posted a few times on these groups
and I could always rely on you :)

the thing I'm looking for is something that would be very simple and
preferrably commandline or input-file driven... so no annotation program
like artemis... I tried out SeqPup (installation was smooth btw), but it
involves a lot of clicking ... and I have quite a few sequences to do ;) 
Maybe there is a way around it by working directly on the
saved-file-format? 

The output of gnomap is the closest to what I'm looking for:
line-box-line pictures
without the sequence (some coordinates would be nice though)... 

(eg
http://iubio.bio.indiana.edu:89/.bin/gnomap?self&spp=weed&chr=ath2&cl=gene&bp=9995089..10004911) 

what kind of input file is used to make these drawings? Is there a way
to separate this part of the program to make a small one that does only
drawing? 

Thanks,

jeroen



Don Gilbert wrote:
> 
> Jeroen Raes asked:
> > Does anybody know of a program to make 'boxed' representations of gene
> > structures in stead of spending hours to draw them?
> 
> There are various programs that do this. Some that I've developed
> include:
> 
> SeqPup, at http://iubio.bio.indiana.edu/soft/molbio/java/apps/seqpup/
> will do some sequence feature drawings for gene sized sequences.
> You can see some example drawings (test*.pdf) in the drawseq subset of it at
> http://iubio.bio.indiana.edu/soft/molbio/java/apps/drawseq/
> Drawing output formats include PDF and GIF.
> 
> For genome-sized sequence maps, I'm working on a program called
> gnomap, which you can see examples of Worm, Fly, Yeast and Weed
> chromosome maps in these organism's folders at
>   http://iubio.bio.indiana.edu/eugenes/
> The program and source to gnomap software is not yet publicly available,
> but let me know if you care to try it.  It isn't designed for
> wide customization of the feature drawings as is the SeqPup/drawseq
> software.
> 
> -- Don
> 
> --
> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> -- gilbertd at bio.indiana.edu

-- 

Jeroen Raes
Research group of Bioinformatics
Department of Plant Genetics   Tel:32.9.264 87 20   Fax:32.9.264 50 08
University of Ghent, K.L. Ledeganckstraat 35, B-9000 GENT, Belgium
Laboratoire Associe de l'INRA
Vlaams interuniversitair Instituut voor Biotechnologie (VIB)
jerae at gengenp.rug.ac.be         http://www.plantgenetics.rug.ac.be







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