[Bioperl-l] display protein/CDS multiple sequence alignments with exon boundaries

Jay Hannah jay at jays.net
Thu Sep 6 15:50:53 EDT 2007


On Wed, 5 Sep 2007, Chris Fields wrote:
> http://www.bioperl.org/wiki/HOWTO_Discussion:Graphics

Wow. That's slick.  :)   Is it possible to zoom in far enough to see the 
individual bases and gaps??

On Tue, 4 Sep 2007, Chris Fields wrote:
> Acc. to the Gbrowse tutorial GBrowse can deal with alignment data:
> http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/docs/tutorial/tutorial.html

Yes, indeed. GBrowse graphs all sorts of amazing things. Specifically, 
this image might be what Albert is looking for:

http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/docs/tutorial/figures/segmented_features2.gif

He'd need to map his exon boundaries from whatever format he has into a 
GFF file (or DAS/BioSQL/Chado/? server, or...?) for GBrowse to munch on.

On Aug 31, 2007, at 4:29 AM, Albert Vilella wrote:
> "Something in the bioperl world without funky external dependencies"

There are still things the long arm of BioPerl justice hasn't reached?   :)

Jay Hannah
http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah



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