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

[Jason Stajich]

Mike - I think the Bio::SeqFeature::Gene::GeneStructure objects *should*
model this for you - GeneStructure will have a reference to all exons, a
transcript is a ordered set of exons.  You could in theory take the unique
set of exons and put them into a single transcript and generate the
introns from that.

Not 100% sure that is the best strategy but might get you on the right
path.

Ensembl has sort of solved this before in their API but unless you are
dealing with genes in an Ensembl-ized genome the Bioperl Gene objects
might work.

-j
On Fri, 22 Nov 2002, Mike Pheasant wrote:

> 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
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu