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Accession number searching in GCG

clark at mshri.utoronto.ca clark at mshri.utoronto.ca
Tue Jun 19 22:06:56 EST 1990


/Does anyone have a VAX/VMS program for use with the Wisconsin
/genetics computer group sotware that can search the keyword index?
/Or one that can search for the accession number?
/STRINGS only searches the DEFINITION line, and FETCH will only
/get an entry based on LOCUSNAME, not accession number.

        Besides using the GCG program strings to get a sequence from its
accession number, you could take advantage of the GenBank email service
which mails you a sequence if you send them the accession number (or locus
name) in the correct format. The response is very fast (typically less than
2 minutes, at least between Toronto Canada and GenBank on Internet), and
the database is always up to date. GenBank will also do a fasta search for
you if you send the sequence, again very quickly, and on their most recent
database. I believe they update it every day, but at worst it's every few
days. For more information on these services, Dave Kristofferson
(kristoff at genbank.bio.net) would probably be the person to get in touch
with. So far as I know, GenBank won't search for keywords, but I would LOVE
it if this were to become available in the future.

        We like these services a lot. So much, in fact, that I've written
some DCL procedures to automate the construction of the mail message in the
format that the GenBank server expects. These are available from your local
friendly server of VAX VMS molecular biology software, or from me directly
if you don't have any other access. Note: These routines require that you
are running the GCG programs on your machine, and have the source code so
that you can link a small Fortran program that does some error-checking.

        BTW, there is a GCG newslist served by utoronto on Netnorth/Bitnet
called info-gcg. You can find out more about it by asking for help from
listserv at utoronto.netnorth, or sending a message to the list owner, John
Cargill (sysjohn at utoroci.netnorth).


Stephen Clark

Samuel Lunenfeld Research Institute
Mt Sinai Hospital, Toronto, Ontario, Canada

clark at mshri.utoronto.ca  (Internet)
clark at utoroci            (Netnorth/Bitnet)

"After all was said and done, more was said than done."




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