[BiO BB] Get Swiss-Port ID from protein names
Dr. Christoph Gille
christoph.gille at charite.de
Mon Aug 7 18:26:50 EDT 2006
>I have a list of proteins (around 70), I need to get their Swissport IDs. I
>don't want to do it manually. Any idea of doing it?
I understand that you have the sequences ?
U could download the Swissprot database as one single file.
Transform this large swissprot file such that there is one line per
entry starting with the ID and containing the entire sequence
HSLV_ECOLI MADFSDFFFASFSDFFAFASDAFSD ....
HSLV_BACSY MADYSEFFFASFSDFFGFASDAFSD ....
You may need basic text processing skills using sed, grep, tr.
Then you can then search in this transformed swissprot file
with fgrep with the 70 sequences as query to identify the respective entry.
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