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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, Kisarazu, Chiba 292, Japan. ynakamu@kazusa.or.jp
Nucleic Acids Research
|January 1, 1997
Summary
This study details codon usage in protein genes, compiling data from GenBank. Organism-specific codon usage is now searchable online, synchronized with GenBank updates.
Area of Science:
- Genomics
- Bioinformatics
- 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 genetic engineering.
Purpose of the Study:
- To calculate and compile codon usage data for individual protein genes across various organisms.
- To make this comprehensive codon usage data easily accessible and searchable for the scientific community.
Main Methods:
- Nucleotide sequences were retrieved from the GenBank Genetic Sequence Database.
- Codon usage for individual genes and the sum of codon usage for each organism were calculated.
- Data was made available through anonymous FTP sites and a searchable website.
Main Results:
- A comprehensive dataset of codon usage for genes in numerous organisms was generated.
- The compiled data was synchronized with major GenBank releases, ensuring up-to-date information.
- A web-based tool was developed for searching codon usage by organism name.
Conclusions:
- The developed resource provides valuable, accessible codon usage data for researchers.
- This facilitates comparative genomics, gene function studies, and codon optimization strategies.
- The synchronized updates ensure the long-term utility of this genomic information resource.