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

Scott Cain cain.cshl at gmail.com
Thu Sep 6 23:20:04 EDT 2007


On Thu, 2007-09-06 at 18:39 -0500, Chris Fields wrote:
> On Sep 6, 2007, at 2:50 PM, Jay Hannah wrote:
> 
> >
> > 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??
> 
> I'm not sure; you can do something like that with GBrowse with some  
> features so there is probably a way to put something together which  
> could do that.

Yeah, if it were me, I would install GBrowse, hack my data into GFF and
use gbrowse_img to generate pictures.  It would probably be easier than
starting from scratch.


> 
> > 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.
> 
> I use segmented SeqFeatures in my example.  The HOWTO also uses a  
> variation ('graded_segments'):
> 
> http://www.bioperl.org/wiki/HOWTO:Graphics#Parsing_Real_BLAST_Output
> 
> The subseqfeatures are colored by score.  Feasibly one could hack  
> this so that the exons/introns have a different 'score', thus  
> displaying different colors.
> 
> > 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
> 
> chris
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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