DATABASE SEARCHING AGAINST DATABASES OF ONLY S. CEREVISIAE SEQUENCES
September 24, 1995
The Saccharomyces Genome Database (SGD) project at Stanford
University announces the availability of a non-redundant database of
S. cerevisiae protein sequences. This non-redundant database is
prepared by processing the open reading frame translations present in
GenBank, known as the GenPept dataset from NCBI, as well as the
SwissProt and PIR protein databases. All S.c. protein sequences from
these three databases are combined. Sequences that are found to be
identical are merged.
The yeast non-redundant protein database is available for searching
via the World Wide Web (WWW) using the BLAST and FASTA programs.
Connect to the Stanford Genome Home Page with the URL:
http://genome-www.stanford.edu/
Look for the "BLAST Searches from SGD" or "FASTA Searches from SGD"
links.
The yeast non-redundant protein database can be retrieved in FASTA
format for use on your computer via Anonymous FTP from:
ftp://genome-ftp.stanford.edu/yeast/yeast_protein/yeast_nrpep.fasta
The BLAST and FASTA searching provided by SGD can also be used against
the S. cerevisiae subset of GenBank. This subset contains all GenBank
sequences identified by their authors as being from S. cerevisiae.
This subset is updated just before the "New Saccharomyces Sequences"
message is sent to the bionet.molbio.yeast group every Tuesday,
Thursday and Saturday. The WWW forms allow several options to be
changed for both BLAST and FASTA searches. The yeast GenBank,
GenPept, and non-redundant protein databases are updated three times a
week, the SwissProt entries are updated once a week, and the PIR
entries are updated with each release. The results of the BLAST and
FASTA searches are presented with WWW links to GenBank, GenPept, EMBL,
SwissProt, PIR/MIPS, and SGD.
We are currently using version 1.4.8MP of the BLAST programs, and
version 2.0u of FASTA. The software used to construct the
non-redundant protein database and the WWW forms was created by Karen
Davis and Mike Cherry. Any questions or comments on this service
should be sent to the e-mail address listed below.
Addresses for the Saccharomyces Genome Database Project (SGD)
e-mail: yeast-curator at genome.stanford.edu
ftp: genome-ftp.stanford.edu
Gopher: genome-gopher.stanford.edu
WWW: http://genome-www.stanford.edu/
Telephone: 415-725-8956
FAX: 415-723-7016
