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Bioinformatics Vol. 17 no. 2 2001
Pages 167-173
© 2001 Oxford University Press

Original Paper

ORI-GENE: gene classification based on the evolutionary tree

Hideaki Mizuno 1,3,4,*, Yoshimasa Tanaka 1, Kenta Nakai 2 and Akinori Sarai 3,*

1 Institute of Biological Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572,
2 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
3 Tsukuba Life Science Center, The Institute of Physical & Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan

Received on January 19, 2000 ; revised on August 19, 2000 ; accepted on October 2, 2000

Motivation: Genome projects have produced large amounts of data on the sequences of new genes whose functions are as yet unknown. The functions of new genes are usually inferred by comparing their sequences with those of known genes, but evaluation of the sequence homology of individual genes does not make the most of the available sequence information. Therefore, new methods and tools for extracting more biological information from homology searches would be advantageous.

Results: We have developed a computational tool, ORI-GENE, to analyze the results of sequence homology searches from the perspective of the evolution of selected sets of new genes. ORI-GENE has a graphical interface and accomplishes two important tasks: first, based on the output of homology searches, it identifies species with similar genes and displays their pattern of distribution on the phylogenetic tree. This function enables one to infer the way in which a given gene may have propagated among species over time. Second, from the distribution patterns, it predicts the point at which a given gene may have been first acquired (i.e. its ‘origin’), then classifies the gene on that basis. Because it makes use of available evolutionary information to show the way in which genes cluster among species, ORI-GENE should be an effective tool for the screening and classification of new genes revealed by genome analysis.

Availability: ORI-GENE is retrievable via the Internet at: http://www.rtc.riken.go.jp/jouhou/ORI-GENE.

Contact: hideaki.mizuno{at}roche.com; sarai{at}rtc.riken.go.jp

* To whom correspondence should be addressed.

4 Present address: Nippon Roche Research Center, 200 Kajiwara, Kamakura, Kanagawa 249-8530, Japan.


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