cherry at GENOME.STANFORD.EDU
Tue May 9 21:30:41 EST 1995
SacchDB 2.4 Quarterly Release from the Saccharomyces Genome Database
The first quarterly release from the Saccharomyces Genome Database
(SGD) at Stanford University are now available using the ACEDB software
developed by Durbin and Thierry-Mieg. This Ace database is called
SacchDB and is available for Macintosh and a variety of UNIX systems,
as well as through the Internet.
A partial list of the new contents of version 2.4 SacchDB:
o All Saccharomyces genes contained in the Registry of Gene Names
on May 6, 1995.
o The regions completed by the systematic sequencing groups are also
placed on the physical map where possible.
o All Saccharomyces DNA sequences contained within GenBank as of
April 18, 1995 are incorporated.
o Gene protein product information obtained from the YPD database
(Garrels and Latter, CSHL) version 3.0 and the literature.
Since the initial version of the database was created (release 2.3
- Jan. 1995), 278 new loci, 193 new sequences, 660 new citations
(including new papers), and 471 new Protein Info entries from YPD v3.0
have been added. This is just a subset of all the new information
Other new features:
The DNA sequences for the ORFs defined by the completed
chromosomes is now available, represented as the name of the ORF
surrounded by plus signs. This sequence is actually more than just
the ORF DNA--it includes 1K upstream and 1K downstream of the ORF.
With Netscape if you select the +ORF+ entries you get the DNA
sequence, whereas with the Macintosh or UNIX ACEDB you just get
another Sequence display. However, if you want the DNA sequence you
can select "EMBL Dump" from the normal Sequence display and then
select the +ORF+ name when requested to choose an object to dump.
From our Web pages you can now find links directly to several
other database servers. Links to the following ten external resources
SWISSPROT Protein database from EMBL (Amos Bairoch)
PIR Protein database from PIR International
GENBANK Nucleic Acid database from NCBI
EMBL Nucleic Acid database from EBI/EMBL
MEDLINE Literature subset from NLM
LISTA Gene Names for Sequenced Genes from Patrick Linder
ENZYME Enzyme Commission reference for catalyses
PROSITE Motif database from Amos Bairoch
YPD Garrels calculated Yeast Protein Database
YEPD Garrels Yeast Experimental Protein (2-D gel) Database
3. A new Systematic Sequencing Table from the WWW. Look for the link
labeled "Systematic Saccharomyces Chromosome Sequencing Projects'
Status" on our home page or follow the URL:
*NOTE* that this table requires a WWW browser that supports HTML 3.0,
such as Netscape 1.1N.
The World Wide Web and Gopher versions of the database are updated
about every week. Since the release of SacchDB 2.3 the network
versions were updated 10 times.
The SacchDB database is available through the Internet using the
World Wide Web from the URL "http://genome-www.stanford.edu/" or using
Internet Gopher to the host named genome-gopher.stanford.edu (port
A downloadable version of the database, for use on a Macintosh or
UNIX computer is available via Anonymous FTP from
genome-ftp.stanford.edu (pub/yeast/SacchDB) or ncbi.nlm.nih.gov
(repository/SacchDB). Please retrieve the file README.installation
first to decide which files you need for your particular system. If
you have SacchDB version 2.3 you should remove that version and
completely reinstall version 2.4 using the directions contained within
the README.installation file.
Please send any suggestions or corrections about the database or
the SGD project to yeast-curator at genome.stanford.edu. Forms are
available from the above Ftp, Gopher, and WWW servers. The forms are
simply suggestions for the types of information we wish to receive
with a gene name registration or submission of mapping data. In the
future electronic Internet forms will be available.
The SGD project at Stanford is funded by a grant from the National
Center for Human Genome Research, National Institutes of Health.
The SGD Project
Mike Cherry, Caroline Adler, Cathy Ball, Karen Davis, Barbara Dunn,
Selina Dwight, Rita Schmidt, Mark Schroeder and David Botstein.
Contacts for the Saccharomyces Genome Database Project (SGD)
E-mail: yeast-curator at genome.stanford.edu
More information about the Yeast