[Bioperl-l] Question on SeqFeature_RelationShip

Peter Cock p.j.a.cock at googlemail.com
Tue Jan 10 13:18:43 EST 2012


On Tue, Jan 10, 2012 at 5:06 PM, lajus <florian.lajus at inria.fr> wrote:
> Hello,
> I am currently working on a refactoring of the Genolevures project
> (http://www.genolevures.org/)
> We are trying to better use bioperl and the bioSQL shema on a postgreSQL
> database.
>
> I have loaded an EMBL file into my BioSQL database (postgres). If I look in
> my database, my bioentry have been added and seqFeatures associated too.
> But it seems that my seqfeature_relationship table is empty.
> I find it strange in so far as there is a relationship between gene and its
> CDS. right?

No, not explicitly. Unlike GFF3 where there can be (and should be)
explicit parent/child links between the gene and CDS, in GenBank
and EMBL feature tables this is implicit only. I don't know if BioPerl
attempts to infer this kind of relationship, and if it did, if that would
get record in the BioSQL tables.

Peter


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