[Bioperl-l] display protein/CDS multiple sequence alignments with exon boundaries
cjfields at uiuc.edu
Mon Sep 10 18:04:14 EDT 2007
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'):
>> 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
> Does anybody know how exon boundaries are displayed in different
Don't know. BTW, apparently there is something being cooked up as an
alignment browser (among other things) 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.
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