We have updated the software for the automatic maintenance of GenBank
from USENET which we have written for VAX/VMS. The new distribution has the
following new features.
- New code to process the check-sequence messages received from GenBank
each week to allow checking the sequence delivery. With this addition
nightly USENET updated banks are essentially verified weekly for completeness.
This makes us feel much better about using the USENET feed.
- Several bug fixes over the last few months including a fairly
substantial reorganization of the code.
- A program called EZFETCH which can be used (by people who run GCG)
to facilitate searching for sequences by primary and secondary accession
numbers and also by locus, and subsequently FETCHing any matches into the
user's current directory.
The general functionality of the programs include: capture of the
daily sequence update feed from USENET. The incorporation of these sequences
into an UPDATE bank, regenerated nightly, and the maintenance of log and
index files from these sequences. Command files which allow the UPDATE bank
to be stripped of sequences incorporated into the latest GenBank tape
distribution based on the closing date of the tape distribution. And now the
weekly check-sequence message processing to provide a degree of UPDATE bank
integrity.
The software can be retrieved by anonymous/FTP from 'mcclb0.med.nyu.edu'
as the single file NIGHTLY_PAK.COM, or from our MAILSERVer by sending mail to
MAILSERV at NYUMED.BITNET with the following two lines in the body of the
message:
SEND NIGHTLY.1
SEND NIGHTLY.2
The distribution is in the form of a VMS_SHARE archive which automatically
unpacks the distribution components.
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|Ross Smith, Cell Biology, NYU Medical Center, 550 First Ave., NYC, 10016|
|Phone: (212) 263-5356: FAX: (212) 263-8139 (Alternate NYUMC) (212) 263-7190|
|E-Mail: SMITH at NYUMED.BITNET (BITNET), SMITH at MCCLB0.MED.NYU.EDU (Internet)|
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