[Bioperl-l] uniprot flatfile extraction

Hilmar Lapp hlapp at gmx.net
Fri Mar 11 13:19:44 EST 2005

Basically everything that's in the UniProt file should be found on the 
RichSeqI object returned from the parser (Bio::SeqIO::swiss). If it's 
in the feature table you'll find it as annotation (tag/value) of the 
features held by the seq object ($seq->get_SeqFeatures). Other stuff 
like dbxrefs are in the annotation bundle ($seq->annotation).


On Wednesday, March 9, 2005, at 06:24  AM, SG Edwards wrote:

> Hi, sorry if this is basic but I've read the documentation and am still
> confused!!
> I wish to extract uniprot flatfile data into my database. I want to 
> get the
> following variables:
> Protein ID, length, description, molecular weight, sequence, comments, 
> cross
> references, disulphide bonds, species, entered date, last modified, 
> last
> annotated, protein synonyms.
> I know that I can get some of these (e.g. protein ID, length) using 
> Bioperl but
> can I get all of the data also or am I better writing my own from 
> scratch?
> Thanks
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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