Related Experiment Videos
The COG database: new developments in phylogenetic classification of proteins from complete genomes
R L Tatusov1, D A Natale, I V Garkavtsev
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Nucleic Acids Research
|January 11, 2000
Summary
The Clusters of Orthologous Groups (COGs) database classifies proteins across genomes. New features enhance its utility for phylogenetic analysis and understanding protein functions.
Area of Science:
- Bioinformatics
- Comparative Genomics
- Protein Phylogeny
Background:
- The Clusters of Orthologous Groups (COGs) database provides a phylogenetic classification of proteins from complete genomes.
- It currently includes 2791 COGs with 45,350 proteins from bacteria, archaea, and yeast.
- A supplement incorporates eukaryotic proteins from Caenorhabditis elegans and Drosophila melanogaster shared with prokaryotes.
Purpose of the Study:
- To enhance the COG database with new features for improved protein classification and analysis.
- To expand the phylogenetic scope by including eukaryotic proteins.
- To refine the COGNITOR program for more accurate protein fitting.
Main Methods:
- Phylogenetic classification of proteins encoded in complete microbial and eukaryotic genomes.
- Development of supplementary datasets including multicellular eukaryotic proteins.
- Enhancement of the COGNITOR program for protein assignment.
- Application of principal component analysis for genome and COG classification.
Main Results:
- The COG database now contains 2791 COGs and 45,350 proteins from 30 genomes.
- Eukaryotic proteins from C. elegans and D. melanogaster have been integrated.
- New features include detailed information pages (structural, functional, literature) for each COG.
- Improvements to the COGNITOR program and new classification methods using principal component analysis.
Conclusions:
- The updated COG database offers enhanced structural and functional insights into protein evolution.
- The inclusion of eukaryotic proteins broadens the comparative genomic scope.
- Advanced computational methods improve the accuracy and utility of the COG resource for phylogenetic studies.