[Bioperl-l] seqs, seqfeatures, locations etc

Brian Osborne bosborne11 at verizon.net
Wed Sep 10 13:34:35 EDT 2008


There is a HOWTO about these Bioperl objects:


I think it addresses your questions.

Brian O.

On Sep 10, 2008, at 11:43 AM, Johnston, Caroline wrote:

> Hello,
> I'm trying to get my head around the various classes for storing  
> sequences, features and locations and was hoping someone could give  
> me some implementation advice:
> I've got a Bio::EnsEMBL::Slice and I want to turn it into a Bio::Seq  
> or SeqFeature object, with Bio::SeqFeature;:Gene::GeneStructure/ 
> Transcript/Exon info attached. I can create a Bio::Seq fine, but I  
> also need to keep track of the chromosomal co-ordinates (chr, start,  
> end, species, strand, genome release, database name) and I can't  
> figure out how to store this in Bioperl. I was thinking that what I  
> needed was some extension of a standard Bio::Seq to have genome- 
> coordinate data attached and associated methods to translate the  
> SeqFeature positions (relative to the Bio::Seq) to genome positions.  
> I guess it's probably already possible to store this type of info in  
> some collection of Bioperl objects, but between Bioperl and the  
> EnsEMBL API I'm getting lost in perl modules. Can someone point me  
> in the right direction?
> Thanks,
> Cass
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