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

Lincoln Stein lstein at cshl.edu
Mon Sep 10 18:09:41 EDT 2007


You can view a simple multiple alignment now. Go to www.wormbase.org, turn
on some of the EST tracks and then zoom down to base pair level.

In bio::graphics, use the "segments" glyph and turn on the -draw_target
option. The features must have DNA attached to them.

What's coming soon is support for MAF format, which provides genome-level
alignments.

Lincoln

On 9/10/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
> On Sep 7, 2007, at 4:20 AM, Albert Vilella wrote:
>
> >>> He'd need to map his exon boundaries from whatever format he has
> >>> into a
> >>> GFF file (or DAS/BioSQL/Chado/? server, or...?) for GBrowse to
> >>> munch on.
> >>
> >> I use segmented SeqFeatures in my example.  The HOWTO also uses a
> >> variation ('graded_segments'):
> >>
> >> http://www.bioperl.org/wiki/HOWTO:Graphics#Parsing_Real_BLAST_Output
> >>
> >> The subseqfeatures are colored by score.  Feasibly one could hack
> >> this so that the exons/introns have a different 'score', thus
> >> displaying different colors.
> >
> >
> > The exon boundary could be a vertical line or a triangular tick or
> > something. I don't know if there is a consensus on this kind of
> > cartoons.
> > Does anybody know how exon boundaries are displayed in different
> > browsers/apps?
>
> Don't know.  BTW, apparently there is something being cooked up as an
> alignment browser (among other things) for GBrowse:
>
> https://www.nescent.org/wg_phyloinformatics/
> PhyloSoC:Phylogenetic_and_Haplotype_Displays_for_GBrowse
>
> Acc. to Lincoln (from his last GBrowse post) there will be a testable
> version within a few weeks or so.  You could always ask more
> questions about it on the GBrowse list.
>
> chris
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>



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Lincoln D. Stein
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