[BiO BB] map swissprot to gi num
sariego9 at yahoo.com
Thu Nov 18 14:24:21 EST 2004
If I understand your need correctly, I may have an
easy solution to the mapping. you can get
the entire swissprot db from ncbi in fasta format, with the ncbi
id in the standard defline, as follows:
>gi|51315800|sp|Q9UPA5|BSN_HUMAN Bassoon protein (Zinc-finger protein 231)
you will notice that the gi and the "Q\w+" identifier
are in the defline. a simple command line perl or
grep to awk will work. if you do not know these,
write me back, I will send you the command line for
the ncbi version of swissprot is available(kinda hard to find)
--- James Stroud <jstroud at mbi.ucla.edu> wrote:
> Hello all,
> I'm looking for a way to completely (if possible) map swissprot accession ids
> to gi numbers. Some type of database file would be best. Most anything will
> Any suggestions?
> Thank you in advance,
> James Stroud, Ph.D.
> UCLA-DOE Institute for Genomics and Proteomics
> 611 Charles E. Young Dr. S.
> MBI 205, UCLA 951570
> Los Angeles CA 90095-1570
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
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