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

[Chris Fields]

On Sep 4, 2007, at 9:31 AM, Jay Hannah wrote:

> On Aug 31, 2007, at 4:29 AM, Albert Vilella wrote:
>> Probably a bit of a long shot but does anyone have code for
>> displaying protein or CDS multiple sequence alignments with the exon
>> boundaries of each gene in the alignment?
>>
>> Something in the bioperl world without funky external dependencies.
>> I think
>> it would be an awesome addition to the howtos.
>>
>> Currently, the Bio::Graphics howto has cdna to genome mapping
>> scripts or
>> blast output scripts, but
>> I couldn't find code for dealing with multiple sequence alignments.
>
> I'm currently under the (potentially uninformed) impression that
> Bio::Graphics and related tools only work with a single  coordinate
> system. I've never seen a multiple sequence alignment example.
>
> (
>    I Google'd for "gbrowse alignment" and hit this:
>    http://maizeapache.danforthcenter.org/cgi-bin/gbrowse.cgi
>
>    Click the second Example link and you'll see exons mapped out.
>
>    But zooming all the way in with all the tracks turned on it looks
> like the AZM tracks are just the coding regions. I don't see any
> multiple sequence alignment...
> )
>
> I doubt that helped.  :)
>
> Jay Hannah
> http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah

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

chris