[Bioperl-l] Re: [Bioperl-announce-l] an extension to Bio::SeqIO

Peili Zhang peili at morgan.harvard.edu
Wed Jun 18 11:04:32 EDT 2003

>> sequence data in any (rich) formats
>> 	 |
>> 	 | via Bio::SeqIO
>> 	 v
>     Bio::Seq->get_SeqFeatures()
>         OR
>      Collection of Bio::SeqFeatureI
>[Actually what's cooler I think is that you don't need Bio::Seq objects or
>anything, just a set of Bio::SeqFeatureI objects. This would mean that
>people could take their GFF files and turn them into chado IFF they are
>rich enough.]

we do want the Bio::Seq objects. for instance, if the Bio::Seq object is a gene, 
we'll want to create a top-level feature of type 'gene' for it in chado, as well 
as loading in its references as feature_pubs, accessions as feature_dbxrefs, 
comments/descriptions/others as featureprops. its gene model features 
(transcripts, exons, CDS's) will hang off of the top-level feature.


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