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Codon usage tabulated from the international DNA sequence databases

Y Nakamura1, K Wada, Y Wada

  • 1National Institute of Genetics and the Graduate University for Advanced Studies, Mishima, Shizuoka, Japan.

Nucleic Acids Research
|January 1, 1996
PubMed
Summary
This summary is machine-generated.

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This study calculated codon usage for 87,602 genes using GenBank data. The Codon Usage Tabulated from various sources (CUTG) Database is now available for organism-specific codon frequency searches online.

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 various fields, including synthetic biology and genetic engineering.

Purpose of the Study:

  • To calculate and compile codon usage data for a large set of genes.
  • To create a searchable database of codon frequencies for different organisms.

Main Methods:

  • Utilized nucleotide sequence data from GenBank (Release 90.0).
  • Analyzed codon usage across 87,602 genes.
  • Developed the Codon Usage Tabulated from various sources (CUTG) Database.

Main Results:

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  • Successfully calculated codon usage for a substantial number of genes.
  • The CUTG Database provides organism-specific codon frequency information.
  • A portion of the database is accessible via a World Wide Web server for easy searching.

    • Conclusions:

    • The establishment of the CUTG Database facilitates research into codon usage patterns.
    • Online accessibility of codon usage data promotes broader scientific inquiry and application.