[BiO BB] Get Swiss-Port ID from protein names
janynan at gmail.com
Wed Aug 9 15:29:34 EDT 2006
Unfortunately, I only have some weak descriptions of protein (protein name).
Is there any way of getting their Swissport IDs?
On 8/7/06, Dr. Christoph Gille <christoph.gille at charite.de> wrote:
> >I have a list of proteins (around 70), I need to get their Swissport IDs.
> >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
> General Forum at Bioinformatics.Org -
> BiO_Bulletin_Board at bioinformatics.org
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