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

[Chris Fields]

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.

> 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