[Bioperl-l] question -- Bio::SeqFeature::Gene::Transcript
hlapp at gmx.net
Sun Nov 4 12:42:13 EST 2007
sorry for taking so long to respond - your email got buried in a pile
while I was away on travel. The Bio::SeqFeature::Gene::* modules were
written mostly with the motivation to have a model that can represent
the results of gene predictors.
GenBank AFAIK doesn't annotate introns explicitly, though they should
be implicit from cDNA (or mRNA? or gene, as you say) features on
genomic sequence. The Bioperl SeqIO parsers won't transform those
into a Bio::SeqFeature::Gene-based model, but instead will yield just
plain Bio::SeqFeatureI objects in a flat array. It's up to subsequent
processing to build these into more hierarchical models.
I'm not sure whether someone's done this already for GenBank-type
feature tables. There is a Unflattener that at least attempts to
build a feature hierarchy from the flat array that's compliant with
the Sequence Ontology (or so I recall).
I'm copying the list in case others have additional suggestions.
On Oct 25, 2007, at 3:40 AM, Stefanie Hartmann wrote:
> Hello Hilmar,
> I have a question about your bioperl module
> I can't figure out how to generate the $gene object for use in this
> @introns = $gene->introns();
> The data I'm working with is a local file in genbank format, and
> I'm interested in extracting intron sequences (and maybe flanking
> exons) for certain genes. I have been trying to get the introns via
> the sequence features ('CDS' or 'gene'), but this has not been
> working. Which approach will I have to take?
> I'd be very grateful if you could point me into the right direction!
> Hope things are going well in Durham! And thank you in advance!
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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