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Bioinformatics Advance Access originally published online on April 7, 2005
Bioinformatics 2005 21(19):3787-3793; doi:10.1093/bioinformatics/bti430
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary

Xizeng Mao 1,{dagger}, Tao Cai 1,{dagger}, John G. Olyarchuk 1 and Liping Wei 1,2,*

1Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing 100871, P.R. China
2Biomedical Informatics, Department of Medicine, Stanford University School of Medicine Stanford, CA 94305, USA

*To whom correspondence should be addressed.

Motivation: High-throughput technologies such as DNA sequencing and microarrays have created the need for automated annotation of large sets of genes, including whole genomes, and automated identification of pathways. Ontologies, such as the popular Gene Ontology (GO), provide a common controlled vocabulary for these types of automated analysis. Yet, while GO offers tremendous value, it also has certain limitations such as the lack of direct association with pathways.

Results: We demonstrated the use of the KEGG Orthology (KO), part of the KEGG suite of resources, as an alternative controlled vocabulary for automated annotation and pathway identification. We developed a KO-Based Annotation System (KOBAS) that can automatically annotate a set of sequences with KO terms and identify both the most frequent and the statistically significantly enriched pathways. Results from both whole genome and microarray gene cluster annotations with KOBAS are comparable and complementary to known annotations. KOBAS is a freely available standalone Python program that can contribute significantly to genome annotation and microarray analysis.

Availability: Supplementary data and the KOBAS system are available at http://genome.cbi.pku.edu.cn/download.html

Contact: weilp{at}mail.cbi.pku.edu.cn

Received on January 18, 2005; revised on March 26, 2005; accepted on April 4, 2005

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