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

[Jay Hannah]

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