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Nucleic Acids Research Advance Access published online on October 8, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn692
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

tRNADB-CE: tRNA gene database curated manually by experts

Takashi Abe1,*, Toshimichi Ikemura1, Yasuo Ohara1, Hiroshi Uehara1, Makoto Kinouchi2, Shigehiko Kanaya3, Yuko Yamada1, Akira Muto4 and Hachiro Inokuchi1

1Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 2Department of Bio-System Engineering, Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, 3Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara and 4Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan

*To whom correspondence should be addressed. Tel: +81 749 64 8100; Fax: +81 749 64 8140; Email: takaabe{at}nagahama-i-bio.ac.jp

Received August 8, 2008. Revised September 22, 2008. Accepted September 25, 2008.

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 ~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.nagahama-i-bio.ac.jp.


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