GenBank now provides an email database searching service using the
BLAST method. The BLAST server is similar to their Fasta server, but has
the advantages of being 10 times faster while maintaining sensitivity, both
strands of the query sequence are searched, and there is no restriction on
the number of concurrent queries. Two disadvantages are that the BLAST
databases are at present only updated quarterly (Fasta databases are
updated daily) and the sequence is required to be in Fasta format, which is
not a supported GCG format. To overcome the latter problem I have written a
small GCG program called Tofasta which converts from GCG format to Fasta
format. I have also written a DCL command procedure called Blastmail to
automate the process of submitting a query to the GenBank server. These
programs are available from the EMBL server (netserv at embl-heidelberg.de),
Dan Davisons's archive (menudo.uh.edu; /pub/gene-server/vms/blast-shell.txt),
Don Gilbert's archive (ftp.bio.indiana.edu) and will probably be at Rob
Harper's archive in Finland soon (nic.funet.fi).
Stephen Clark
clark at galen.oci.utoronto.ca (Internet)
clark at utoroci (Netnorth/Bitnet)
"For what it is worth, many of the legends accompanying figures in this journal
are not very different, although we take some care to provide each sentence
with a verb if the author has overlooked the need for one." -J.Maddox, Nature.
