Sequence Analysis & Tools
search, display, analyze sequences

Maps
yeast chromosome maps

Literature
yeast reference guide

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register a yeast gene

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FTP data, lists, tables

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colleagues, meetings

Help
SGD help resources

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send data and suggestions

About SGD
information about SGD and staff; citing SGD

New interactive GO tutorial available at SGD

SGD has created a tutorial to familarize users with the Gene Ontology (GO) and how it is used at SGD. The tutorial gives an overview of GO and highlights pages and tools at SGD that use GO annotations. In addition, the tutorial provides links to other sites that may help users take advantage of the power of GO. For more information about GO, see the GO home page or the SGD help page for GO. (Posted August 14, 2002)

Protein property data for entire proteome available for download

Predicted protein properties such as molecular weight, pI, CAI, protein length, etc. for all S. cerevisiae ORFs are available on the SGD ftp site, in the protein_info/ directory. The README file in the same directory describes the file format, which can be read by Excel or any other text editor. (Posted August 13, 2002)

Budding Yeast Sequence Alignments Available

Genome wide alignments between S. cerevisiae and S. paradoxus, S. mikatae, and S. bayanus are now available via SGD. These pre-publication data are part of a larger work by Manolis Kamvysselis, Nick Patterson, Eric Lander and others at the Whitehead Institute for Biomedical Research. Sequence and alignments are available for individual genes. You can retrieve alignment information for your favorite gene either by searching for it, or by choosing the "Other budding yeasts homologs" option under "Comparison Resources" on any Locus Page. For more information on this new resource, please see the accompanying help page. (Posted July 29, 2002)
Update: Protein sequence alignment has now been incoporated in this tool. Clicking on an ORF from another species will retrieve the protein sequence alignment. (Posted August 9, 2002)

New BLAST Resource Available

Developed from an independent sequencing effort, this BLAST resource at Washington University in St. Louis (provided by Paul Cliften and Mark Johnston) allows users to find regions of homology between S. cerevisiae and five related species, S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri. (Posted July 31, 2002)

New Gene Ontology (GO) tool at SGD

SGD now provides a tool, the GO Term Mapper, that maps the granular GO terms used to annotate a list of genes to their more general parent terms (ie. GO Slim terms). This tool allows you to look at broad biological processes, molecular functions, or cellular components in which a list of genes is involved or localized. For more information on this tool, see the help page. For more information on the GO project, see the GO home page or the SGD help page for GO. (Posted July 29, 2002)

SGD links to the GRID database of interactions

SGD now links from each locus page to the GRID database of genetic and physical interactions. GRID, developed in Mike Tyers group, contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND. These links are available from the Interactions pull down menu on the right side of each locus page. Thanks to Bobby-Joe Breitkreutz for providing information about generating the links. (Posted July 23, 2002)

VectorDB now hosted at SGD

The VectorDB, created by Stephen Misener, is a database containing information about many commonly used plasmid vectors; this database is now hosted at SGD. You can browse yeast vectors, search the names and descriptions of the vectors, and also BLAST using the vector sequences as the target dataset. More features will be coming soon! (Posted July 16, 2002)

Major reorganization of the SGD ftp site

The SGD ftp site, where you can download data contained within SGD, has been reorganized to make it much easier to find various data files (for eg, sequence data, GO annotations). Most of the data is now centrally located in the data_download directory. In addition, in each directory, older versions of the files are stored in an archive directory. The previous file locations will eventually be removed, though most are currently linked to the new file locations. The two directories that have been moved without links are the data from the yeast-worm comparison and the vector sequences, now found in the data_download/sequence_similarity and data_download/sequence directories, respectively. As always, please contact us if you have any questions or suggestions. (posted July 15, 2002)

2002 Yeast Genetics and Molecular Biology Meeting Abstracts Online

The 2002 YGM Meeting abstracts are available from two sites :

SGD
Genetics Society of America

The meeting will happen this July 30-August 4 at the University of Wisconsin, Madison. The GSA site, http://www.yeast-meet.org/, provides all meeting information. (updated July 12, 2002)

New sequence retrieval software installed at SGD

New sequence retrieval software has been implemented at SGD. The new software should allow for faster retrieval of DNA and protein sequences. Please let us know if you find any problems. (Posted July 8, 2002)

   The Saccharomyces Genome Database (SGD^TM) project is funded by the National Human Genome Research Institute at the US National Institutes of Health.   The SGD^TM is in the Department of Genetics at the School of Medicine, Stanford University. The trademark on SGD^TM is held by Stanford University.

Database Copyright © 1997-2002 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. How to cite SGD.