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TMBETA-GENOME


NAR Molecular Biology Database Collection entry number 938
Gromiha M.M.1, Yabuki Y.1, Kundu S.2, Suharnan S.2 and Suwa M.1
1Computational 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
2Axiohelix Pvt. Limited, Tokyo, Japan

Database Description

TMBETA-GENOME is a database for annotated beta-barrel membrane proteins in genomic sequences using statistical methods and machine learning algorithms (1). The statistical methods are based on amino acid composition (2), reside pair preference (3) and motifs (4). In machine learning techniques, the combination of amino acid and dipeptide compositions has been used as main attributes (5). In addition, annotations have been made using a “new approach” based on the (i) identification of beta-barrel membrane proteins using residue pair preferences and (ii) exclusion of globular and transmembrane helical (TMH) proteins using sequence identity with known structures in Protein Data Bank and sequences in SWISS-PROT, and SOSUI, a program for detecting TMH proteins. A web interface has been developed for identifying the annotated beta-barrel membrane proteins in all known genomes. The users have the feasibility of selecting the genome from the three kingdoms of life, arachaea, bacteria and eukaryote, and five different methods. It may be noted that the new approach considerably reduced the number of false positives and it has the ability of picking up most of the real beta-barrel membrane proteins. TMBETA-GENOME has the annotated data for 275 completed genomes, including 23 genomes from archaea, 237 from bacteria and 15 from eukaryote. Further, for a genome that have different chromosomes (for example, human genome has 24 chromosomes) the data for each chromosome is given individually. Further, the statistics for all genomes have been provided along with the links to different algorithms and related databases.

References

1. Gromiha MM, Yabuki, Y, Kundu S, Suharnan S, Suwa M. (2007) TMEBTA-GENOME: a database for annotated beta barrel membrane proteins in genomic sequences. Nucleic Acids Res. 35 (Database issue): in press.
2. Gromiha MM, Suwa M. A simple statistical method for discriminating outer membrane proteins with better accuracy. Bioinformatics. 2005; 21:961-968.
3. Gromiha MM, Ahmad S, Suwa M. Application of residue distribution along the sequence for discriminating outer membrane proteins. Comput Biol Chem. 2005; 29: 135-42.
4. Gromiha MM. Motifs in outer membrane protein sequences: Applications for discrimination. Biophys Chem. 2005; 117, 65-71.
5. Park KJ, Gromiha MM, Horton P, Suwa M. Discrimination of outer membrane proteins using support vector machines. Bioinformatics. 2005; 21:4223-9.

Subcategory: Protein structure

Go to the abstract in the NAR 2007 Database Issue.
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