The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community

Nucleic Acids Research

Volumn 38, Issue SUPPL.1, 2009, Pages

  Arnaud, Martha B ^a   Chibucos, Marcus C ^b   Costanzo, Maria C ^a   Crabtree, Jonathan ^b   Inglis, Diane O ^a   Lotia, Adil ^a   Orvis, Joshua ^b   Shah, Prachi ^a   Skrzypek, Marek S ^a   Binkley, Gail ^a   Miyasato, Stuart R ^a   Wortman, Jennifer R ^b   Sherlock, Gavin ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASPERGILLUS; ASPERGILLUS GENOME DATABASE; ASPERGILLUS NIDULANS; FUNGAL GENETICS; GENETIC DATABASE; GENOMICS; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INFORMATION SERVICE; MOLECULAR BIOLOGY; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; FUNGAL GENE; FUNGAL GENOME; GENETICS; INTERNET; METABOLISM; METHODOLOGY; NUCLEIC ACID DATABASE; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE;

ASPERGILLUS;

FUNGAL PROTEIN;

ASPERGILLUS NIDULANS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; FUNGAL PROTEINS; GENES, FUNGAL; GENETICS; GENOME, FUNGAL; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MODELS, GENETIC; PHENOTYPE; PROTEIN STRUCTURE, TERTIARY; SOFTWARE;

EID: 75549090164     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp751     Document Type: Article

References (21)

1. Galagan, J.E., Calvo, S.E., Cuomo, C., Ma, L.J., Wortman, J.R., Batzoglou, S., Lee, S.I., Basturkmen, M., Spevak, C.C., Clutterbuck, J. et al. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature, 438, 1105-1115.
2. Machida, M., Asai, K., Sano, M., Tanaka, T., Kumagai, T., Terai, G., Kusumoto, K., Arima, T., Akita, O., Kashiwagi, Y. et al. (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature, 438, 1157-1161.
3. Nierman, W.C., Pain, A., Anderson, M.J., Wortman, J.R., Kim, H.S., Arroyo, J., Berriman, M., Abe, K., Archer, D.B., Bermejo, C. et al. (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature, 438, 1151-1156.
4. Mabey Gilsenan, J.E., Atherton, G., Bartholomew, J., Giles, P.F., Attwood, T.K., Denning, D.W. and Bowyer, P. (2009) Aspergillus genomes and the Aspergillus cloud. Nucleic Acids Res., 37, D509-D514.
5. 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. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
6. Wortman, J.R., Gilsenan, J.M., Joardar, V., Deegan, J., Clutterbuck, J., Andersen, M.R., Archer, D., Bencina, M., Braus, G., Coutinho, P. et al. (2009) The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet. Biol., 46(Suppl. 1), S2-S13.
7. 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.
8. Crabtree, J., Angiuoli, S.V., Wortman, J.R. and White, O.R. (2007) Sybil: methods and software for multiple genome comparison and visualization. Methods Mol. Biol., 408, 93-108.
9. Consortium, T.G.O. (2001) Creating the gene ontology resource: design and implementation. Genome Res., 11, 1425-1433.
10. Aslett, M. and Wood, V. (2006) Gene ontology annotation status of the fission yeast genome: preliminary coverage approaches 100%. Yeast, 23, 913-919.
11. Bult, C.J., Eppig, J.T., Kadin, J.A., Richardson, J.E. and Blake, J.A. (2008) The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res., 36, D724-D728.
12. Hong, E.L., Balakrishnan, R., Dong, Q., Christie, K.R., Park, J., Binkley, G., Costanzo, M.C., Dwight, S.S., Engel, S.R., Fisk, D.G. et al. (2008) Gene ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res., 36, D577-D581.
13. 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.
14. Sprague, J., Bayraktaroglu, L., Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Knight, J. et al. (2008) The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res., 36, D768-D772.
15. Tweedie, S., Ashburner, M., Falls, K., Leyland, P., McQuilton, P., Marygold, S., Millburn, G., Osumi-Sutherland, D., Schroeder, A., Seal, R. et al. (2009) FlyBase: enhancing Drosophila gene ontology annotations. Nucleic Acids Res., 37, D555-D559.
16. Twigger, S.N., Shimoyama, M., Bromberg, S., Kwitek, A.E. and Jacob, H.J. (2007) The Rat Genome Database, update 2007-easing the path from disease to data and back again. Nucleic Acids Res., 35, D658-D662.
17. Arnaud, M.B., Costanzo, M.C., Shah, P., Skrzypek, M.S. and Sherlock, G. (2009) Gene ontology and the annotation of pathogen genomes: the case of Candida albicans. Trends Microbiol., 17, 295-303.
18. Costanzo, M.C., Skrzypek, M.S., Nash, R.S., Wong, E.D., Binkley, G., Engel, S.R., Hitz, B.C., Hong, E.L. and Cherry, J.M. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database, 2009, Article ID bap001.
19. Wapinski, I., Pfeffer, A., Friedman, N. and Regev, A. (2007) Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics, 23, i549-i558.
20. Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M. and Sherlock, G. (2004) GO::TermFinder-open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics, 20, 3710-3715.
21. Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610.