[Bioperl-l] Merging exons in all transcripts for a gene

[Mike Pheasant]

Hi,

I'm interested in noncoding regions of genes with alternate transcripts.
I'd like to merge all exons in all transcripts of one gene to come up
with a new *non-overlapping* set of start/end coordinates of all
sequences that end up in any mRNA for that gene. From this I can then
find all intronic sequences that are non-coding and end up in no mRNA. 

For example, an intron on one transcript may overlap an exon on another
transcript. I only want that part of the introns that overlap no exons.

It seems non-trivial but not impossible and so before I attempt it I'd
appreciate if anyone knows of existing code which does this. Doesn't
appear to be in BioPerl at the moment.

Thanks,

Mike.

_____________
Mike Pheasant
PhD Student
Institute for Molecular Bioscience
University of Queensland, Australia
Mobile: 0405 609 541
Fax: +61-7-3319 6268
http://www.imb.uq.edu.au