Paper Info
Title
tRNADB-CE: tRNA gene database curated manually by experts.
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 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.
Year
DOI
Venue
2009
10.1093/nar/gkn692
NUCLEIC ACIDS RESEARCH
DocType
Volume
Issue
Journal
37
Database issue
ISSN
Citations 
PageRank 
0305-1048
3
0.76
References 
Authors
4
9
Name
Order
Citations
PageRank
Takashi Abe1405.52
Toshimichi Ikemura27916.80
Yasuo Ohara3294.60
Hiroshi Uehara4164.29
Makoto Kinouchi5102.35
Shigehiko Kanaya624923.88
Yuko Yamada781.53
Akira Muto8101.90
Hachiro Inokuchi981.53