Nucleic Acids Research Advance Access originally published online on May 25, 2007
Nucleic Acids Research 2007 35(Web Server issue):W182-W185; doi:10.1093/nar/gkm321
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W182-W185
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
KAAS: an automatic genome annotation and pathway reconstruction server
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
*To whom Correspondence should be addressed. Tel: +81 774 38 3270; Fax: +81 774 38 3269; Email: kanehisa{at}kuicr.kyoto-u.ac.jp
Received January 30, 2007. Revised March 31, 2007. Accepted April 17, 2007.
The number of complete and draft genomes is rapidly growing in recent years, and it has become increasingly important to automate the identification of functional properties and biological roles of genes in these genomes. In the KEGG database, genes in complete genomes are annotated with the KEGG orthology (KO) identifiers, or the K numbers, based on the best hit information using Smith–Waterman scores as well as by the manual curation. Each K number represents an ortholog group of genes, and it is directly linked to an object in the KEGG pathway map or the BRITE functional hierarchy. Here, we have developed a web-based server called KAAS (KEGG Automatic Annotation Server: http://www.genome.jp/kegg/kaas/) i.e. an implementation of a rapid method to automatically assign K numbers to genes in the genome, enabling reconstruction of KEGG pathways and BRITE hierarchies. The method is based on sequence similarities, bi-directional best hit information and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated KEGG GENES database.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. Faust, D. Croes, and J. van Helden In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools' Bioinformatics, December 1, 2009; 25(23): 3202 - 3205. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Kashima, Y. Yamanishi, T. Kato, M. Sugiyama, and K. Tsuda Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach Bioinformatics, November 15, 2009; 25(22): 2962 - 2968. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Li, X. Li, Y. Miao, Q. Wang, W. Jiang, C. Xu, J. Li, J. Han, F. Zhang, B. Gong, et al. SubpathwayMiner: a software package for flexible identification of pathways Nucleic Acids Res., October 1, 2009; 37(19): e131 - e131. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Zaburannyy, B. Ostash, and V. Fedorenko TTA Lynx: a web-based service for analysis of actinomycete genes containing rare TTA codon Bioinformatics, September 15, 2009; 25(18): 2432 - 2433. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Mazumdar, E. S. Snitkin, S. Amar, and D. Segre Metabolic Network Model of a Human Oral Pathogen J. Bacteriol., January 1, 2009; 191(1): 74 - 90. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Martin, S. Abubucker, T. Wylie, Y. Yin, Z. Wang, and M. Mitreva Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics Nucleic Acids Res., January 1, 2009; 37(suppl_1): D571 - D578. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. M. Kim, S. Sung, G. Caetano-Anolles, J. Y. Han, and H. Kim An approach of orthology detection from homologous sequences under minimum evolution Nucleic Acids Res., October 1, 2008; 36(17): e110 - e110. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Okuda, T. Yamada, M. Hamajima, M. Itoh, T. Katayama, P. Bork, S. Goto, and M. Kanehisa KEGG Atlas mapping for global analysis of metabolic pathways Nucleic Acids Res., July 1, 2008; 36(suppl_2): W423 - W426. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. May, S. Wienkoop, S. Kempa, B. Usadel, N. Christian, J. Rupprecht, J. Weiss, L. Recuenco-Munoz, O. Ebenhoh, W. Weckwerth, et al. Metabolomics- and Proteomics-Assisted Genome Annotation and Analysis of the Draft Metabolic Network of Chlamydomonas reinhardtii Genetics, May 1, 2008; 179(1): 157 - 166. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Kanehisa, M. Araki, S. Goto, M. Hattori, M. Hirakawa, M. Itoh, T. Katayama, S. Kawashima, S. Okuda, T. Tokimatsu, et al. KEGG for linking genomes to life and the environment Nucleic Acids Res., January 11, 2008; 36(suppl_1): D480 - D484. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Brilli, R. Fani, and P. Lio Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes Brief Bioinform, January 1, 2008; 9(1): 34 - 45. [Abstract] [Full Text] [PDF]
|
|