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About SGD

General Content

The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae. This database includes a variety of genomic and biological information and is maintained and updated by SGD curators. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae. This task was transferred to the SGD by Dr. Robert Mortimer in early 1994. We have also compiled a set of general guidelines to gene naming that may be of help to researchers who are naming new S. cerevisiae genes.

Funding Source & Location

The SGD is funded by the National Human Genome Research Institute at the US National Institutes of Health. The SGD is in the Department of Genetics at the School of Medicine, Stanford University.

Viewing SGD

SGD is best viewed using Safari 3.0, Firefox 3.0, Internet Explorer 7, or higher.

Database Software/Documentation/Specifications

• SGD Hardware

  The production SGD database runs on 2 SunFire T2000 servers, each with 32GB of RAM and an 8-core CPU with 4 threads per core. The load is balanced between these two servers with a Foundry ServerIron XL switch. Similar SunFire T2000 servers are used for development and testing.

  The Textpresso application runs on 2 Dell servers. The Textpresso indexes are generated on a Dell 1850 server with with 4GB RAM and 2 dual-core CPUs. The production web server and main PDF storage is on a Dell 2850 server with with 4GB RAM and 2 CPUs.

  The Pathway Tools application runs on a Dell 1850 with 11GB RAM and 2 CPUs.

• Database Management System (DBMS)

  SGD uses the Oracle Server Enterprise Edition 10.2.0.4. Table specifications, schema diagrams, and business rules for the SGD database can be found at SGD Schema Specifications. Before moving to Oracle in 2000, SGD used AceDB as its database software.

• System software

The T2000 servers run SunOS 5.10 (aka Solaris 10).

The Dell servers run Linux Red Hat Enterprise Linux 5.2.

• Other software packages and libraries

• Perl 5.8.8
• DBI 1.607
• DBD::Oracle 1.22
• BioPerl 1.5.1 with patches
• Apache Web Server 2.2.4

• Third-party applications

• WU-BLAST 2.0MP-WashU 4-May-2006
• BLAT 32
• FASTA 35.3.6
• GBrowse 1.68
• Pathway Tools 10.0
• Textpresso 2.0.0

Retrieving Data

The data stored in SGD can be searched using the SGD Full Search or downloaded. SGD contains links to other yeast information sources, such as the General Yeast Topics wiki page and the Yeast BioSci Archive. Information about the SGD staff and web page usage statistics are available as well.

Contacting SGD

You may send the SGD curators comments or questions via a Web form. Alternatively, send electronic mail to yeast-curator@genome.stanford.edu or call us at (650) 725-8956.

Return to Saccharomyces Genome Database