Skip to main content
Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2002 Jun;3(3):282–288. doi: 10.1002/cfg.175

Website Review: How to Get the Best From Fission Yeast Genome Data

Valerie Wood 1, Jürg Bähler 1,
PMCID: PMC2447279  PMID: 18628858

Abstract

Researchers are increasingly depending on various centralized resources to access the vast amount of information reported in the literature and generated by systematic sequencing and functional genomics projects. Biological databases have become everyday working tools for many researchers. This dependency goes both ways in that the databases require continuous feedback from the research community to maintain accurate, reliable, and upto- date information. The fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genome era of this popular model organism. Here, we provide an overview of relevant databases available, or being developed, together with a compilation of Internet resources containing useful information and tools for fission yeast.

Full Text

The Full Text of this article is available as a PDF (96.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Apweiler R., Attwood T. K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M. D. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 2001 Jan 1;29(1):37–40. doi: 10.1093/nar/29.1.37. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ashburner M., Ball C. A., Blake J. A., Botstein D., Butler H., Cherry J. M., Davis A. P., Dolinski K., Dwight S. S., Eppig J. T. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25–29. doi: 10.1038/75556. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Ball C. A., Jin H., Sherlock G., Weng S., Matese J. C., Andrada R., Binkley G., Dolinski K., Dwight S. S., Harris M. A. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80–81. doi: 10.1093/nar/29.1.80. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bateman Alex, Birney Ewan, Cerruti Lorenzo, Durbin Richard, Etwiller Laurence, Eddy Sean R., Griffiths-Jones Sam, Howe Kevin L., Marshall Mhairi, Sonnhammer Erik L. L. The Pfam protein families database. Nucleic Acids Res. 2002 Jan 1;30(1):276–280. doi: 10.1093/nar/30.1.276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C. A., Causton H. C. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001 Dec;29(4):365–371. doi: 10.1038/ng1201-365. [DOI] [PubMed] [Google Scholar]
  6. Ding D. Q., Tomita Y., Yamamoto A., Chikashige Y., Haraguchi T., Hiraoka Y. Large-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion genomic DNA library. Genes Cells. 2000 Mar;5(3):169–190. doi: 10.1046/j.1365-2443.2000.00317.x. [DOI] [PubMed] [Google Scholar]
  7. Dwight Selina S., Harris Midori A., Dolinski Kara, Ball Catherine A., Binkley Gail, Christie Karen R., Fisk Dianna G., Issel-Tarver Laurie, Schroeder Mark, Sherlock Gavin. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1;30(1):69–72. doi: 10.1093/nar/30.1.69. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Eisen Jonathan A. Brouhaha over the other yeast. Nature. 2002 Feb 21;415(6874):845–848. doi: 10.1038/nature725. [DOI] [PubMed] [Google Scholar]
  9. Gene Ontology Consortium Creating the gene ontology resource: design and implementation. Genome Res. 2001 Aug;11(8):1425–1433. doi: 10.1101/gr.180801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Le Crom Stéphane, Devaux Frédéric, Jacq Claude, Marc Philippe. yMGV: helping biologists with yeast microarray data mining. Nucleic Acids Res. 2002 Jan 1;30(1):76–79. doi: 10.1093/nar/30.1.76. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M. A., Barrell B. Artemis: sequence visualization and annotation. Bioinformatics. 2000 Oct;16(10):944–945. doi: 10.1093/bioinformatics/16.10.944. [DOI] [PubMed] [Google Scholar]
  12. Wixon Jo. Featured organism: Schizosaccharomyces pombe, the fission yeast. Comp Funct Genomics. 2002;3(2):194–204. doi: 10.1002/cfg.92. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Wood V., Gwilliam R., Rajandream M-A, Lyne M., Lyne R., Stewart A., Sgouros J., Peat N., Hayles J., Baker S. The genome sequence of Schizosaccharomyces pombe. Nature. 2002 Feb 21;415(6874):871–880. doi: 10.1038/nature724. [DOI] [PubMed] [Google Scholar]

Articles from Comparative and Functional Genomics are provided here courtesy of Wiley

RESOURCES