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TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences
M Michael Gromiha1, Yukimitsu Yabuki, Srinesh Kundu
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. michael-gromiha@aist.go.jp
Nucleic Acids Research
|November 8, 2006
Summary
TMBETA-GENOME is a new database for identifying beta-barrel membrane proteins in genomes. It uses statistical and machine learning methods for accurate annotation across all kingdoms of life.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Beta-barrel membrane proteins are crucial in biological membranes.
- Accurate identification of these proteins across diverse genomes is challenging.
- Existing databases lack comprehensive annotation for beta-barrel proteins.
Purpose of the Study:
- To develop a comprehensive database, TMBETA-GENOME, for annotated beta-barrel membrane proteins.
- To provide a user-friendly web interface for identifying these proteins in genomic sequences.
- To facilitate research on the function and distribution of beta-barrel proteins.
Main Methods:
- Utilized statistical methods including amino acid composition, residue pair preferences, and motif analysis.
- Employed machine learning techniques using amino acid and dipeptide compositions as key attributes.
- Implemented annotation criteria for precise identification of beta-barrel proteins, excluding globular and helical types.
Main Results:
- Developed TMBETA-GENOME, a database of annotated beta-barrel membrane proteins.
- Created a web interface enabling genome selection from archaea, bacteria, and eukaryota.
- Integrated five distinct identification methods with comprehensive genome statistics and database links.
Conclusions:
- TMBETA-GENOME offers a valuable resource for beta-barrel membrane protein annotation.
- The database enhances the study of protein distribution and function across life's kingdoms.
- Freely accessible online, promoting broader scientific accessibility and research.
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