[Bioperl-l] bioperl-db: exporting data

Johan Viklund johan.viklund at gmail.com
Tue Jul 5 11:01:40 EDT 2005


I'm trying to add COG annotations from Entrez Gene to sequences (from
refseq in genbank format) I have in a biosql database (on mysql). The
problem is I can't get them out again with the bioentry2flat.pl script
(the bioentries appears without what i've added).

I don't use bioperl for this (i've got ~40000 COG annotations (linked
to GeneIDs)). Instead I add it to the seqfeature_qualifer_value table
similar to the way GeneID:s are represented (as far as i've figured),
with term_id corresponding to db_xref, the same seqfeature_id as the
GeneID had and rank i've tried a few different variations but none
seem to work (the first free that's larger than GeneID and 1).

How should I add this annotation to the database so it gets exported
when I use bioperl?

I've also got another question: What is rank for?

Johan Viklund
E-mail: <johan.viklund.0705 at student.uu.se>
        <johan.viklund at gmail.com>

More information about the Bioperl-l mailing list