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. 2009 Jan;37(Database issue):D163-8.
doi: 10.1093/nar/gkn692. Epub 2008 Oct 8.

tRNADB-CE: tRNA gene database curated manually by experts

Takashi Abe  1 , Toshimichi Ikemura, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi
Affiliations

tRNADB-CE: tRNA gene database curated manually by experts

Takashi Abe et al. Nucleic Acids Res. 2009 Jan.

Abstract

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 approximately 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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Figures

Figure 1.
Figure 1.
Workflow of searching for tRNA genes.
Figure 2.
Figure 2.
Result of tRNA gene search. Numbers in Venn diagrams show numbers of tRNA genes found by individual programs and those in parenthesis show numbers after manual checks by experts. Abbreviations and definitions are the followings: SE, sensitivity level = 100 × (the number of reliable tRNAs predicted by one program)/(the number of all reliable tRNAs); SP, specificity level = 100 × (the number of reliable tRNAs predicted by one program)/(the number of candidate tRNAs predicted by the respective program). Because tRNAfinder can not predict tRNAs with intron, SE and SP are not presented for archaea.
Figure 3.
Figure 3.
tRNADB-CE interface snapshots.
See this image and copyright information in PMC

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