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Codon usage tabulated from the international DNA sequence databases
Y Nakamura1, T Gojobori, T Ikemura
1Laboratory of Gene Structure 2, Kazusa DNA Research Institute, 1532-3 Yana, Kisarazu, Chiba 292, Japan. ynakamu@kazasu.or.jp
Nucleic Acids Research
|February 21, 1998
Summary
The CUTG database provides comprehensive codon usage data for genes across various organisms, sourced from GenBank. This resource facilitates research into genetic code variations and evolutionary patterns.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- Codon usage bias is a significant factor in gene expression and protein synthesis.
- Understanding codon usage patterns is crucial for fields like synthetic biology and comparative genomics.
- Existing databases may lack comprehensive or up-to-date codon usage information.
Purpose of the Study:
- To establish a comprehensive and accessible database of codon usage for genes.
- To facilitate the study of codon usage patterns across diverse organisms.
- To provide a searchable web interface for accessing codon usage data.
Main Methods:
- Collected full-length protein gene sequences from the GenBank database.
- Calculated codon usage for individual genes and aggregated usage for each organism.
- Developed a searchable website for accessing and analyzing the compiled data.
Main Results:
- The CUTG database offers codon usage data for numerous organisms.
- Data is synchronized with major GenBank releases, ensuring up-to-date information.
- The database is accessible via anonymous FTP and a dedicated website.
Conclusions:
- The CUTG database serves as a valuable resource for researchers studying codon usage.
- Its comprehensive nature and accessibility promote further investigation into genetic code.
- Facilitates comparative analysis of codon usage across the tree of life.