Nucleic Acids Research, 2000, Vol. 28, No. 1 292
© 2000 Oxford University Press
Codon usage tabulated from international DNA sequence databases: status for the year 2000
Laboratory of Gene Structure 2, Kazusa DNA Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan and 1National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
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.
* To whom correspondence should be addressed. Tel: +81 438 52 3935; Fax: +81 438 52 3934; Email: ynakamu@kazusa.or.jp
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|
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|
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 |
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|
|
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|
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