clark@MSHRI.UTORONTO.CA (02/07/90)
Archive-name: genbank/05-Feb-90
Original-posting-by: clark@MSHRI.UTORONTO.CA
Original-subject: RE: Up-to-Date Sequence Data
Archive-site: genbank.bio.net [134.172.1.160]
Reposted-by: emv@math.lsa.umich.edu (Edward Vielmetti)
Lisa H. Beeler writes:
/I wrote last week seeking information about translating IG sequence data to
/GCG format sequence data. I received a response from Dana Fowlkes about
/getting the Genbank and EMBL sequences weekly via FTP on the Genbank.bio.net.
/I hate to expose my ignorance, but I do not know how to use this technology.
Don't worry, lot's of people don't know how to ftp, including me,
but it doesn't bother me since I don't have access from my site anyway.
However, GenBank will provide searching services and sequence data
via email, so you don't need ftp. For a Fasta search, send your sequence to
search@genbank.bio.net. To retrieve a sequence, send a one-line message to
retrieve@genbank.bio.net. The one line should contain just the locus name
of the sequence you want, or the accession number. Unfortunately you can
only get one at a time. Also, send the message HELP to either address and
you will get back full instructions on how to use the services. They both
work fine. In fact, I'm trying to get our users to stop doing fasta
searches on our VAX because it only takes 1/2 hour for GenBank to return
the results of their search, and their database is much much more up to
date than is ours.
By the way, I have written a couple of command procedures to
automate the procedure of sending search and retrieval requests to GenBank.
If anyone would like copies, drop me a note.
To convert an IG sequence to GCG format, the program is called
FROMIG, and to go the opposite direction, use TOIG.
Stephen Clark
clark@mshri.utoronto.ca (Internet)
sinai@utoroci (Netnorth/Bitnet)
"We should be quite remiss not to emphasize that despite the popularity of
secondary structural prediction schemes, and the almost ritual performance
of these calculations, the information available from this is of limited
reliability. This is true even of the best methods now known, and much more
so of the less successful methods commonly available in sequence analysis
packages. Running a secondary structure prediction on a newly-determined
sequence just because everyone else does so, is to be deplored, and the
fact that the results of such predictions are generally ignored is
insufficient justification for doing and publishing them."
- Arthur Lesk, 1988