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Nucleic Acids Research Advance Access published online on November 6, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl805
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© 2006 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.

Database Issue

TMBETA-GENOME: database for annotated ß-barrel membrane proteins in genomic sequences

M. Michael Gromiha1,*, Yukimitsu Yabuki1, Srinesh Kundu2, Sivasundaram Suharnan2 and Makiko Suwa1

1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan 2 Axiohelix Pvt Limited Tokyo, Japan

*To whom correspondence should be addressed. Tel: +81 3 3599 8046; Fax: +81 3 3599 8081; Email: michael-gromiha{at}aist.go.jp

Received August 7, 2006. Revised September 20, 2006. Accepted September 29, 2006.

We have developed the database, TMBETA-GENOME, for annotated ß-barrel membrane proteins in genomic sequences using statistical methods and machine learning algorithms. The statistical methods are based on amino acid composition, reside pair preference and motifs. In machine learning techniques, the combination of amino acid and dipeptide compositions has been used as main attributes. In addition, annotations have been made using the criterion based on the identification of ß-barrel membrane proteins and exclusion of globular and transmembrane helical proteins. A web interface has been developed for identifying the annotated ß-barrel membrane proteins in all known genomes. The users have the feasibility of selecting the genome from the three kingdoms of life, archaea, bacteria and eukaryote, and five different methods. Further, the statistics for all genomes have been provided along with the links to different algorithms and related databases. It is freely available at http://tmbeta-genome.cbrc.jp/annotation/.


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