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

Nucleic Acids Res. 2007 Jan;35(Database issue):D314-6. doi: 10.1093/nar/gkl805. Epub 2006 Nov 6.

Abstract

We have developed the database, TMBETA-GENOME, for annotated beta-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 beta-barrel membrane proteins and exclusion of globular and transmembrane helical 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, 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/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Artificial Intelligence
  • Data Interpretation, Statistical
  • Databases, Protein*
  • Genomics
  • Internet
  • Membrane Proteins / chemistry*
  • Membrane Proteins / genetics*
  • Protein Structure, Secondary
  • Sequence Analysis, Protein
  • User-Computer Interface

Substances

  • Membrane Proteins