[Bioperl-l] loading sprot.dat

Brian Osborne brian_osborne at cognia.com
Thu Jan 8 10:55:43 EST 2004


Some of the data in a SwissProt file is parsed into Features, some of it
into Annotations (Swissprot entries are RichSeq objects, like Genbank and
EMBL entries). So probably you'll want to look at the Feature-Annotation
HOWTO. Unfortunately there are no Swissprot examples there but the logic
will be the same, open the file with SeqIO and print out specific entries,
or portions of entries, with the desired characteristics. Perhaps the SeqIO
HOWTO would be useful as well...

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Robinson, Peter
Sent: Thursday, January 08, 2004 10:18 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] loading sprot.dat

Hi all,

I would like to load the contents of the Swiss-Prot file sprot.dat into a
mysql database. Since I have a relatively specific question, I would like to
use a databse of my own design and just extract portions of the relevant
entries from sprot.dat rather than the whole thing.
I would appreciate it if someone could point me to an example script for
this kind of thing. I did not see anything like this in my perusals of the
archives or google, please forgive me if this question has been asked



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