gmane.comp.lang.perl.bio.general

seqs, seqfeatures, locations etc

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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Brian Osborne | 10 Sep 19:34

Re: seqs, seqfeatures, locations etc

Cass,

There is a HOWTO about these Bioperl objects:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

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

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