I have the following input:
(1) List of protein-coding gene models in GFF3 format (2) List of protein features of these genes (e.g. protein domains or transmembrane regions), with coordinates on the protein sequence-level.
As output, I would like to have an image that shows all gene models drawn to scale side-by-side, with protein features mapped onto coding exons. Different feature types should be drawn in different colors (configurable), and features are allowed to span exon-exon junctions. Ideally, the generation of such an image can be completely automated.
Can anyone suggest a program that can do this?
FeatureStack and decorated_gene are now available from CPAN as well: http://search.cpan.org/~chrisfr/
A paper describing this module is now published in Bioinformatics: http://bioinformatics.oxfordjournals.org/content/early/2012/09/27/bioinformatics.bts572.short