Gene annotation and pathway mapping in KEGG

Methods in Molecular Biology

Volumn 396, Issue , 2007, Pages 71-91

  Aoki Kinoshita, Kiyoko F ^a   Kanehisa, Minoru ^a  

^a NONE

Author keywords

Gene annotation; KAAS; KEGG; KEGG orthology; KO; Pathway mapping

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER INTERFACE; GENETIC DATABASE; MOLECULAR GENETICS;

AMINO ACID SEQUENCE; DATABASES, GENETIC; MOLECULAR SEQUENCE DATA; USER-COMPUTER INTERFACE;

EID: 36549002108     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-515-6:71     Document Type: Article

References (12)

1. Kanehisa, M., Goto, S., Hattori, M., et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-D357.
2. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277-D280.
3. Pruitt, K. D., Tatusova, T., and Maglott, D. R. (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33, D501-D504.
4. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Wheeler, D. L. (2006) GenBank. Nucleic Acids Res. 34, D16-D20.
5. Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
6. Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A. (2002) The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46.
7. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A., and Kanehisa, M. (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. in press.
8. Tatusov, R. L., Fedorova, N. D., Jackson, J. D., et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41.
9. (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 34, D322-D326.
10. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
11. Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
12. Aoki, K. F. and Kanehisa, M. (2005) in Current Protocols in Bioinformatics, (Andreas D. and Baxevanis, L. D. S., ed.), John Wiley and Sons, Ltd.