[Bioperl-l] Genebank mRNAs

[Castle, John]

Hi BioPerl,

Thanks for the good perl scripts.  I'm having trouble with them and was
wondering if someone could address this problem or refer me to someone else.

I'm trying to read in files in GenBank format and output the various mRNA
sequences for each GenBank record.  Can I do this with the BioPerl modules?
(Side note - the SeqIO scripts choke on the headers contained in the NCBI
Genbank flat files.)

A given GenBank sequence may have several mRNAs, these "features" can be
alternate splice forms and contain differing amounts of the total sequence;
this is specified by the "join" lines in the Genbank records.

When I read in a Genbank file with subfeatures, I think the modules
currently bless the subfeatures as Bio::SeqFeature::Generic objects.
Unfortunately, when I ask for the sequence of a mRNA feature, it returns the
total sequence, not the mRNA sequence.

Any ideas?

Thanks,
	John Castle


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