[BiO BB] map swissprot to gi num

[Diego Martinez]

Dear James,
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
it.
the ncbi version of swissprot is available(kinda hard to find) 
at:
ftp://ftp.ncbi.nih.gov/blast/db/FASTA/swissprot.gz

goodluck.

Diego




--- 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 
> do.
> 
> Any suggestions?
> 
> Thank you in advance,
> James
> 
> -- 
> 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
> http://www.jamesstroud.com/
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 


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