Codon usage tabulated from international DNA sequence databases: Status for the year 2000

Yasukazu Nakamura*, Takashi Gojobori, Toshimichi Ikemura

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

771 Scopus citations

Abstract

The frequencies of each of the 257,468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by 8792 organisms has also been calculated. The data files can be obtained from the anonymous ftp sites of DDBJ, Kazusa and EBI. A list of the codon usage of genes and the sum of the codons used by each organism can be obtained through the web site http://www.kazusa.or.jp/codon/. The present study also reports recent developments on the WWW site. The new web interface provides data in the CodonFrequency-compatible format as well as in the traditional table format. The use of the database is facilitated by keyword based search analysis and the availability of codon usage tables for selected genes from each species. These new tools will provide users with the ability to further analyze for variations in codon usage among different genomes.

Original languageEnglish (US)
Pages (from-to)292
Number of pages1
JournalNucleic Acids Research
Volume28
Issue number1
StatePublished - Jan 1 2000
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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