[Bioperl-l] display protein/CDS multiple sequence alignments with exon boundaries
cjfields at uiuc.edu
Thu Sep 6 19:39:07 EDT 2007
On Sep 6, 2007, at 2:50 PM, Jay Hannah wrote:
> On Wed, 5 Sep 2007, Chris Fields wrote:
> Wow. That's slick. :) Is it possible to zoom in far enough to
> see the
> individual bases and gaps??
I'm not sure; you can do something like that with GBrowse with some
features so there is probably a way to put something together which
could do that.
> On Tue, 4 Sep 2007, Chris Fields wrote:
>> Acc. to the Gbrowse tutorial GBrowse can deal with alignment data:
> Yes, indeed. GBrowse graphs all sorts of amazing things. Specifically,
> this image might be what Albert is looking for:
> 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
The subseqfeatures are colored by score. Feasibly one could hack
this so that the exons/introns have a different 'score', thus
displaying different colors.
> On Aug 31, 2007, at 4:29 AM, Albert Vilella wrote:
>> "Something in the bioperl world without funky external dependencies"
> There are still things the long arm of BioPerl justice hasn't
> reached? :)
> Jay Hannah
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