Codon Usage Database

Codon Usage Database provides comprehensive codon frequency data derived from 257,468 complete protein-coding sequences (CDSs) from the GenBank DNA sequence database, representing the sum of codons used by 8,792 organisms to support analysis of codon usage patterns across taxonomic divisions.

Key Features:

• Extensive Data Compilation: Aggregates codon counts and frequency data calculated from 257,468 complete CDSs extracted from GenBank across 8,792 organisms and multiple taxonomic divisions.
• Data Formats: Outputs data in CodonFrequency-compatible formats and traditional table formats.
• Keyword-Based Search Functionality: Enables keyword-based queries to retrieve targeted codon usage data.
• Codon Usage Tables: Provides detailed codon usage tables for selected genes from each species to support comparative analyses.

Scientific Applications:

• Comparative Genomics: Analyze variations in codon usage across genomes to investigate evolutionary processes and genetic diversity.
• Gene Expression Optimization: Inform codon optimization for heterologous protein production in biotechnology and synthetic biology.
• Mutation Analysis: Examine effects of mutations on codon usage and potential impacts on protein synthesis relevant to disease mechanisms and genetic disorders.

Methodology:

Compilation of complete CDSs from GenBank and calculation of summed codon counts and frequency distributions across organisms, with keyword-based search and export in CodonFrequency-compatible and table formats.