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

Albert Vilella avilella at gmail.com
Fri Sep 7 05:20:01 EDT 2007


>
> > 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?


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