Skip Navigation

SGD - Saccharomyces Genome Database


NAR Molecular Biology Database Collection entry number 357
Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM.
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

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. Physical and genetic interactions, both from large scale studies and those from experiments focused on a single protein have been expanded. The reference sequence, and its annotation, from the laboratory strain S288c continues to be updated.

Acknowledgements

Major funding for the SGD project is via a P41 resource grant from NHGRI (5P41HG001315-11). Additional support for Gene Ontology annotation is partially supported via the Gene Ontology Consortium grant, a P41 resource from NHGRI (5P41HG002273-05).

References

1. Balakrishnan, R., Christie, K.R., Costanzo, M.C., Dolinski, K., Dwight, S.S., Engel, S.R., Fisk, D.G., Hirschman, J.E., Hong, E.L., Nash, R., Oughtred, R., Skrzypek, M., Theesfeld, C.L., Binkley, G., Dong, Q., Lane, C., Sethuraman, A., Weng, S., Botstein, D., Cherry, J.M. (2005) Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Research 33:D374-377.
2. Christie, K.R., Weng, S., Balakrishnan, R., Costanzo, M.C., Dolinski, K., Dwight, S.S., Engel, S.R., Feierbach, B., Fisk, D.G., Hirschman, J.E., Hong, E.L., Issel-Tarver, L., Nash, R., Sethuraman, A., Starr, B., Theesfeld, C.L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Botstein, D., Cherry, J.M. (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Research 32:D311-314
3. Weng, S., Dong, Q., Balakrishnan, R., Christie, K., Costanzo, M., Dolinski, K., Dwight, S.S., Engel, S., Fisk, D.G., Hong, E., Issel-Tarver, L., Sethuraman, A., Theesfeld, C., Andrada, R., Binkley, G., Lane, C., Schroeder, M., Botstein, D., Cherry, J.M. (2003) Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Research 31:216-218
4.. 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
5. 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
6. The Gene Ontology Consortium (2001) Creating the Gene Ontology Resource: Design and Implementation. Genome Research 11:1425-1433.


Go to the abstract in the NAR 2014 Database Issue.
Oxford University Press is not responsible for the content of external internet sites