Related Experiment Videos
Codon usage tabulated from international DNA sequence databases: status for the year 2000
Y Nakamura1, T Gojobori, T Ikemura
1Laboratory of Gene Structure 2, Kazusa DNA Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan. ynakamu@kazusa.or.jp
Nucleic Acids Research
|December 11, 1999
Summary
This study compiles codon usage frequencies for over 257,000 protein-coding sequences from GenBank, enabling analysis of variations across diverse genomes. Enhanced web tools facilitate keyword searches and data access for researchers.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Codon usage bias is a fundamental aspect of genome evolution and gene expression.
- Understanding codon frequencies is crucial for fields like synthetic biology and protein engineering.
Purpose of the Study:
- To compile and provide access to a comprehensive dataset of codon usage frequencies for complete protein-coding sequences (CDSs).
- To develop enhanced web-based tools for analyzing and visualizing codon usage data across various organisms and genomes.
Main Methods:
- Compiled codon frequencies for 257,468 complete CDSs from the GenBank DNA sequence database.
- Calculated the sum of codons used by 8,792 organisms.
- Developed a new web interface offering data in CodonFrequency-compatible and traditional table formats, with keyword-based search functionality.
Main Results:
- A large-scale dataset of codon usage frequencies and sums is now available.
- The updated WWW site provides improved data accessibility and analysis tools.
- Users can now analyze codon usage variations among different genomes more effectively.
Conclusions:
- The comprehensive codon usage database and associated web tools facilitate deeper analysis of genomic variations.
- These resources support research in molecular evolution, gene expression regulation, and synthetic biology.