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Saccharomyces Genome Database

http://genome-www.stanford.edu/Saccharomyces/

Dolinski, K., Balakrishnan, R., Christie, K., Costanzo, M., Dwight, S., Engel, S., Fisk, D., Hong, E., Issel-Tarver, L., Sethuraman, A., Theesfeld, C., Binkely, G., Lane, C., Schroeder, M., Dong, S., Kaloper, M., Weng, S., Andrada, R., Botstein, D., Cherry, J.M.

Department of Genetics, Stanford University, Stanford, CA 94305-5120 USA

Contact   cherry@stanford.edu


Database Description

The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it. Information in SGD has traditionally been organized around a gene; each gene in the genome has a central locus page, where you can find Gene Ontology (GO) annotations, DNA and protein sequence data and analysis tools, phenotype information, large scale expression results, and several other types of biological information. Literature curation has been at the heart of the SGD project, and literature citations are provided where available. In addition to manual literature curation, SGD is testing methods such as scanning full text articles for keywords, to provide information at a more detailed level in an efficient way. SGD is also currently developing additional tools that are less gene-centric, which can be utilized for more global types of analysis. In addition, as more genomes are completely sequenced, comparative genomics will become an even more powerful tool; thus, SGD is exploring ways of presenting the results of these studies.

Recent Developments

Alignments of four Saccharomyces genus allows identification of evolutionary conservation of protein sequences. This information will be used to update ORF annotations.

Acknowledgements

Major funding from NHGRI for the SGD and for Gene Ontology Consortium. We also thank Incyte Genomics for a gift to work on Gene Ontology.

REFERENCES

Dwight, S.S., Harris, M.A., Dolinski, K., Ball, C.A., Binkley, G., Christie, K.R., Fisk, D.G., Issel-Tarver, L., Schroeder, M., Sherlock, G., Sethuraman, A., Weng, S., Botstein, D. and J.M. Cherry (2002) Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Research 30:69-72.
Issel-Tarver, L., Christie, K.R., Dolinski, K., Andrada, R., Balakrishnan, R., Ball, C.A., Binkley, G., Dong, S., Dwight, S.S., Fisk, D.G., Harris, M., Schroeder, M., Sethuraman, A., Tse, K., Weng, S., Botstein, D. and J.M. Cherry (2002) The Saccharomyces Genome Database. Methods in Enzymology 350:329-346
The Gene Ontology Consortium (2001) Creating the Gene Ontology Resource: Design and Implementation. Genome Research 11:1425-1433.

Category   Genomic Databases

Go to the abstract in the NAR 2003 Database Issue.

 

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