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

Albert Vilella avilella at gmail.com
Wed Sep 5 09:31:24 EDT 2007


Awesome!!

Thanks Chris!

On 9/5/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
> You mean something like this?
>
> http://www.bioperl.org/wiki/HOWTO_Discussion:Graphics
>
> chris
>
> On Sep 5, 2007, at 4:42 AM, Albert Vilella wrote:
>
> > 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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> >>
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


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