[Bioperl-l] display protein/CDS multiple sequence alignments with exon boundaries
avilella at gmail.com
Wed Sep 5 05:42:37 EDT 2007
A couple of examples:
treefam has exon boundary and PFAM domain mappings
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,
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:
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
More information about the Bioperl-l