Codon usage tabulated from the international DNA sequence databases; its status 1999

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Codon usage bias is a fundamental aspect of gene expression.
• Understanding codon frequencies is crucial for various molecular biology applications.
• Databases of genetic information are essential for large-scale biological research.

Purpose of the Study:

• To compile and provide comprehensive codon usage data for a large number of genes and organisms.
• To make this genetic information easily accessible to the scientific community.
• To facilitate research in areas such as gene expression, protein synthesis, and evolutionary biology.

Main Methods:

• Extraction of complete protein-coding gene sequences (CDS) from the GenBank DNA sequence database.
• Compilation of codon frequencies for individual genes and the sum of codon usage for 7,434 organisms.
• Data organization and provision through anonymous FTP sites (DDBJ, DISC, EBI).
• Development of a web-based search interface for organism-specific codon usage data.

Main Results:

• A dataset containing codon usage frequencies for 206,526 complete protein-coding genes.
• Calculated codon usage sums for 7,434 distinct organisms.
• Accessible data files available via anonymous FTP from major biological databases.
• A searchable website (http://www.dna.affrc.go.jp//CUTG.html) enabling retrieval of codon usage data by organism name.

Conclusions:

• The creation of a comprehensive and accessible codon usage database supports diverse research endeavors.
• Facilitated access to genetic information aids in comparative genomics and evolutionary studies.
• The provided resources empower researchers to investigate codon bias and its implications in molecular biology.