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

Chris Fields 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'):
>>
>> 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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