Codon usage tabulated from international DNA sequence databases: status for the year 2000
Codon usage tabulated from international DNA sequence databases: status for the year 2000
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DOI：
10.1093/nar/28.1.292
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发表时间：
2000-01-01
影响因子：
14.9
通讯作者：
Ikemura, T
中科院分区：
文献类型：
--
作者：
Nakamura, Y;Gojobori, T;Ikemura, T
257 468个完整的蛋白质编码序列（CDSs）的频率已经从GenBank DNA序列数据库的分类分类中编译出来。8792种生物使用的密码子总数也被计算出来。数据文件可以从DDBJ、Kazusa和EBI的匿名ftp站点获得，基因密码子使用列表和每个生物体使用密码子的总和可以通过http://www.kazusa.or.jp/codon/网站获得。本研究还报告了万维网网站的最新发展。新的web界面提供密码子-频率兼容格式以及传统表格格式的数据。基于关键词的搜索分析和每个物种所选基因的密码子使用表的可用性促进了数据库的使用。这些新工具将为用户提供进一步分析不同基因组中密码子使用差异的能力。
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 Codon-Frequency-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.