tRNADB-CE: tRNA gene database curated manually by experts

被引：21

作者：

Abe, Takashi ^{[1
]}

Ikemura, Toshimichi ^{[1
]}

Ohara, Yasuo ^{[1
]}

Uehara, Hiroshi ^{[1
]}

Kinouchi, Makoto ^{[2
]}

Kanaya, Shigehiko ^{[3
]}

Yamada, Yuko ^{[1
]}

Muto, Akira ^{[4
]}

Inokuchi, Hachiro ^{[1
]}

机构：

[1] Nagahama Inst Biosci & Technol, Shiga, Japan

[2] Yamagata Univ, Grad Sch Sci & Engn, Dept Biosyst Engn, Yamagata 990, Japan

[3] Nara Inst Sci & Technol, Grad Sch Informat Sci, Nara, Japan

[4] Hirosaki Univ, Fac Agr & Life Sci, Aomori, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2009年 / 37卷

关键词：

GENOMIC SEQUENCE; LATERAL TRANSFER; INTRONS; PROGRAM;

D O I：

10.1093/nar/gkn692

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We constructed a new large-scale database of tRNA genes by analyzing 534 complete genomes of prokaryotes and 394 draft genomes in WGS (Whole Genome Shotgun) division in DDBJ/EMBL/GenBank and approximately 6.2 million DNA fragment sequences obtained from metagenomic analyses. This exhaustive search for tRNA genes was performed by running three computer programs to enhance completeness and accuracy of the prediction. Discordances of assignment among three programs were found for similar to 4% of the total of tRNA gene candidates obtained from these prokaryote genomes analyzed. The discordant cases were manually checked by experts in the tRNA experimental field. In total, 144 061 tRNA genes were registered in the database 'tRNADB-CE', and the number of the genes was more than four times of that of the genes previously reported by the database from analyses of complete genomes with tRNAscan-SE program. The tRNADB-CE allows for browsing sequence information, cloverleaf structures and results of similarity searches among all tRNA genes. For each of the complete genomes, the number of tRNA genes for individual anticodons and the codon usage frequency in all protein genes and the positioning of individual tRNA genes in each genome can be browsed. tRNADB-CE can be accessed freely at http://trna.nagahamaibio.ac.jp.

引用

页码：D163 / D168

页数：6

共 19 条

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