[Biopython] Local Uniprot

[Sauer, David]

Hi all,
I have a script where I query the UniProt website for particular protein entries, following BioPython and UniProt’s own python access notes. However, as a way to be polite, I wait a few seconds between queries, but this makes my script fairly slow. I would like to keep the database locally, but the only downloads I can find for the UniProtKB are as two huge xml files for Swiss-Prot and TrEMBL. I am unclear how to parse these compared to the individual protein xml files on the website, which are easily parsable by BioPython.

Does anyone have guidance on parsing and running the UniProtKB locally?

Thanks in advance!

David Sauer

Da-Neng Wang Lab
Structural Biology Program
New York University School of Medicine

Publications via Google Scholar<http://scholar.google.com/citations?user=F9G61tAAAAAJ&hl=en&oi=ao>
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