ORI-GENE: A Tool for Gene Classification and Prediction of Function Based on the Evolutionary Tree
Hideaki Mizuno1, 3$, Yoshimasa Tanaka1, Kenta Nakai2 and Akinori Sarai3#
1Institute of Biological sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki, 305-8572 Japan.
2Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan.
3Tsukuba Life Science Center, The Institute of Physical & Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074 Japan.
$Present address: Kamakura Research Laboratories, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa, 247-8530 Japan.
#Present address: Dept. Biochemical Engineering and Science, Kyushu Institute of Technology (KIT),680-4 Kawazu, Iizuka, 820-8502 Japan.
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 classification and screening of new genes revealed by genome analysis.
Last updated: 2009/06/10