Saccharomyces Genome Database: a resource for fungal comparative genomics.
Maria C. Costanzo (1), Rama Balakrishnan (1), Karen R. Christie (1), Kara Dolinski (2), Selina S. Dwight (1), Stacia R. Engel (1), Dianna G. Fisk (1), Jodi E. Hirschman (1), Eurie L. Hong (1), Robert Nash (1), Anand Sethuraman (1), Barry Starr (1), Chandra L. Theesfeld (1), Rey Andrada (1), Gail Binkley (1), Qing Dong (1), David Botstein (2), and J. Michael Cherry (1)
(1) Department of Genetics, Stanford U. School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5120, USA;
(2) Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Washington Rd., Princeton, NJ 08544, USA
The Saccharomyces Genome Database (SGD; .) is a comprehensive compilation of genome, gene, and protein information for S. cerevisiae. SGD offers several sequence comparison tools that facilitate analysis of conservation across species. The Synteny Viewer displays alignments between S. cerevisiae chromosomes and those of closely related Saccharomyces species. The Fungal Alignment Viewer displays ClustalW alignments of each S. cerevisiae protein with its potential orthologs from several Saccharomyces species. A Fungal BLAST tool allows comparison of any input sequence to a wide variety of fungal sequences, with the ability to generate custom alignments by species. BLASTP alignments of each S. cerevisiae protein with the most similar proteins in other model organisms are available, with links to the corresponding model organism databases. Finally, to facilitate finding more distantly related proteins, results of a pre-computed, periodically updated PSI-BLAST analysis of each S. cerevisiae protein vs. all proteins in GenBank are also presented. All information at SGD is freely available, both via the web interface and in downloadable files. SGD is funded by the US National Human Genome Research Institute.
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