YOGY: A web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms

Nucleic Acids Research

Volumn 34, Issue WEB. SERV. ISS., 2006, Pages

  Penkett, Christopher J ^a   Morris, James A ^a   Wood, Valerie ^a   Bähler, Jürg ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EUKARYOTE; EUKARYOTIC ORTHOLOGY; INFORMATION PROCESSING; INTERNET; MUS MUSCULUS; NOMENCLATURE; ORTHOLOGY; PLASMODIUM FALCIPARUM; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; ANIMAL; COMPUTER INTERFACE; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; HUMAN; LINGUISTICS; MOUSE; RAT; SEQUENCE HOMOLOGY; SYSTEM ANALYSIS;

ARABIDOPSIS THALIANA; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTA; HOMO SAPIENS; MUS MUSCULUS; PLASMODIUM FALCIPARUM; RATTUS NORVEGICUS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES; SCHIZOSACCHAROMYCES POMBE;

PROTEIN;

ANIMALS; DATABASES, GENETIC; HUMANS; INTERNET; MICE; PROTEINS; RATS; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE; VOCABULARY, CONTROLLED;

EID: 33747870202     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl311     Document Type: Article

References (30)

1. Henikoff,S., Greene,E.A., Pietrokovski,S., Bork,P., Attwood,T.K. and Hood,L. (1997) Gene families: the taxonomy of protein paralogs and chimeras. Science, 278, 609-614.
2. Chervitz,S.A., Aravind,L., Sherlock,G., Ball,C.A., Koonin,E.V., Dwight,S.S., Harris,M.A., Dolinski,K., Mohr,S., Smith,T. et al. (1998) Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science, 282, 2022-2028.
3. Koonin,E.V. (2005) Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet., 39, 309-338.
4. Fitch,W.M. (2000) Homology: a personal view on some of the problems. Trends Genet., 16, 227-231.
5. Tatusov,R.L., Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V., Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
6. Tatusov,R.L., Koonin,E.V. and Lipman,D.J. (1997) A genomic perspective on protein families. Science, 278, 631-637.
7. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
8. Remm,M., Storm,C.E. and Sonnhammer,E.L. (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol., 314, 1041-1052.
9. Sonnhammer,E.L. and Koonin,E.V. (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet., 18, 619-620.
10. O'Brien,K.P., Remm,M. and Sonnhammer,E.L. (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res., 33, D476-D480.
11. Wheeler,D.L., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Edgar,R., Federhen,S. et al. (2005) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 33, D39-D45.
12. Chen,F., Mackey,A.J., Stoeckert,C.J.,Jr and Roos,D.S. (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res., 34, D363-D368.
13. Li,L., Stoeckert,C.J.,Jr and Roos,D.S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189.
14. Wood,V. (2006) Schizosaccharomyces pombe comparative genomics; from sequence to systems. In Sunnerhagen,P. and Piskur,J. (eds), Comparative Genomics Using Fungi as Models (Series: Topics in Current Genetics). Springer, Berlin, Vol 15, pp. 233-285.
15. Harris,M.A., Clark,J., Ireland,A., Lomax,J., Ashburner,M., Foulger,R., Eilbeck,K., Lewis,S., Marshall,B., Mungall,C. et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 32, D258-D261.
16. Birney,E., Andrews,D., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cox.T., Cunningham,F., Curwen,V., Cutts,T. et al. (2006) Ensembl 2006. Nucleic Acids Res., 34, D556-D561.
17. Wu,C.H., Apweiler,R., Bairoch,A., Natale,D.A., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez,R. et al. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res., 34, D187-D191.
18. Eppig,J.T., Bult,C.J., Kadin,J.A., Richardson,J.E., Blake,J.A., Anagnostopoulos,A., Baldarelli,R.M., Baya,M., Beal,J.S., Bello,S.M. et al. (2005) The Mouse Genome Database (MGD): from genes to mice - a community resource for mouse biology. Nucleic Acids Res., 33, D471-D475.
19. de la Cruz,N., Bromberg,S., Pasko,D., Shimoyama,M., Twigger,S., Chen,J., Chen,C.F., Fan,C., Foote,C., Gopinath,G.R. et al. (2005) The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res., 33, D485-D491.
20. Rhee,S.Y., Beavis,W., Berardini,T.Z., Chen,G., Dixon,D., Doyle,A., Garcia-Hernandez,M., Huala,E., Lander,G., Montoya,M. et al. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res., 31, 224-228.
21. Grumbling,G. and Strelets,V. (2006) FlyBase: anatomical data, images and queries. Nucleic Acids Res., 34, D484-D488.
22. Schwarz,E.M., Antoshechkin,I., Bastiani,C., Bieri,T., Blasiar,D., Canaran,P., Chan,J., Chen,N., Chen,W.J., Davis,P. et al. (2006) WormBase: better software, richer content. Nucleic Acids Res., 34, D475-D478.
23. Hertz-Fowler,C., Peacock,C.S., Wood,V., Aslett,M., Kerhornou,A., Mooney,P., Tivey,A., Berriman,M., Hall,N., Rutherford,K. et al. (2004) GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res., 32, D339-D343.
24. 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. et al. (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res., 32, D311-D314.
25. Kersey,P.J., Duarte,J., Williams,A., Karavidopoulou,Y., Birney,E. and Apweiler,R. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics, 4, 1985-1988.
26. Rustici,G., Mata,J., Kivinen,K., Lio,P., Penkett,C.J., Burns,G., Hayles,J., Brazma,A., Nurse,P. and Bahler,J. (2004) Periodic gene expression program of the fission yeast cell cycle. Nature Genet., 36, 809-817.
27. Mata,J., Lyne,R., Burns,G. and Bähler,J. (2002) The transcriptional program of meiosis and sporulation in fission yeast. Nature Genet., 32, 143-714.
28. Chen,D., Toone,W.M., Mata,J., Lyne,R., Burns,G., Kivinen,K., Brazma,A., Jones,N. and Bähler,J. (2003) Global transcriptional responses of fission yeast to environmental stress. Mol. Biol. Cell, 14, 214-229.
29. Byrne,K.P. and Wolfe,K.H. (2006) Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. Nucleic Acids Res., 34, D452-455.
30. Sherman,D., Durrens,P., Iragne,F., Beyne,E., Nikolski,M. and Souciet,J.L. (2006) Ge'nolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. Nucleic Acids Res., 34, D432-D435.