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

Albert Vilella avilella at gmail.com
Wed Sep 5 05:42:37 EDT 2007


A couple of examples:

http://www.treefam.org/cgi-bin/alnview.pl?ac=TF105041

treefam has exon boundary and PFAM domain mappings

http://www.ensembl.org/Homo_sapiens/genetreeview?gene=ENSG00000139618

here the tree is shown as well, but the idea would be to plot the alignment

So it's more "show me the multiple CDS/protein alignment" rather than "show
my aligned CDS/proteins wrt my reference genome"

I think it would be quite neat to have this as a bioperl howto,

Comments?

    Albert.

On 9/4/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> 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
>
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