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Bioinformatics Advance Access published online on October 21, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp594
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

G-compass: A web-based comparative genome browser between human and other vertebrate genomes

Yoshihiro Kawahara 1,2, Ryuichi Sakate 3, Akihiro Matsuya 1,4, Katsuhiko Murakami 1,3, Yoshiharu Sato 3, Hao Zhang 1,5, Takashi Gojobori 3,6, Takeshi Itoh 2 and Tadashi Imanishi 3,*

1Japan Biological Information Research Center, Japan Biological Informatics Consortium, Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan
2Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
3Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan
4Government & Public Corporation Information Systems, Hitachi, Co., Ltd., Toyo 2-4-18, Koto-ku, Tokyo 135-8633, Japan
5BITS, Co., Ltd. A402 Sanko Building, 20-3 Shimotogari, Nagaizumi-cho, Suntou-gun, Shizuoka 411-0943, Japan
6Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan

*To whom correspondence should be addressed. Tadashi Imanishi, E-mail: t.imanishi{at}aist.go.jp


  Abstract

Summary: G-compass is designed for efficient comparative genome analysis between human and other vertebrate genomes. The current version of G-compass allows us to browse two corresponding genomic regions between human and another species in parallel. One-to-one evolutionarily conserved regions (i.e., orthologous regions) between species are highlighted along the genomes. Information such as locations of duplicated regions, copy number variations, and mammalian ultra-conserved elements is also provided. These features of G-compass enable us to easily determine patterns of genomic rearrangements and changes in gene orders through evolutionary time. Since G-compass is a satellite database of H-InvDB, which is a comprehensive annotation resource for human genes and transcripts, users can easily refer to manually curated functional annotations and other abundant biological information for each human transcript. G-compass is expected to be a valuable tool for comparing human and model organisms and promoting the exchange of functional information.

Availability: G-compass is freely available at http://www.h-invitational.jp/g-compass/.

Contact: t.imanishi{at}aist.go.jp

Associate Editor: Prof. Dmitrij Frishman

Received on June 11, 2009; revised on September 24, 2009; accepted on October 12, 2009

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