The tRNA Gene DataBase Curated by Experts "tRNADB-CE" was constructed by analyzing 6,024 complete and 67,053 draft genomes of Bacteria and Archaea, 876 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones. This exhaustive search for tRNA genes from DDBJ/EMBL/GenBank was performed by running tRNAscan-SE
, a computer program widely used for tRNA gene searches, in combination with ARAGORN
, to enhance completeness and accuracy of the prediction. Discordance of assignment by these three programs was found for approximately 4 % of the total of tRNA gene candidates. These discordant cases were manually checked by experts in the tRNA experimental field. In addition, tRNA genes of Archaea obtained from SPLITSdb
The 4,171,385 tRNA genes in total (363,553, 3,638,722, 4601, 3534, 4266 and 156,709 genes from complete prokaryote genomes, draft prokaryote genomes, virus genomes, eukaryote genomes, chloroplast genomes and metagenomes, respectively) were registered in the present database; and sequence information, clover-leaf structure, and results of similarity search among tRNA genes can be browsed. For each of the completely sequenced genome, the number of anticodon and the codon usage frequency and the positioning of individual tRNA genes in each genome along with those of neighboring tRNA genes can be browsed. In the database, users can conduct various sequence analyses including sequence similarity search and oligonucleotide pattern search. This comprehensive database should contribute to various studies of tRNA gene evolution and diversity and of tRNA molecular biology. In the future, we will add all eukaryotic tRNA genes under the collaboration of experts of various eukaryotic tRNA research fields.
About the workflow of searching for tRNA genes in this database.
Takashi Abe, Hachiro Inokuchi, Yuko Yamada, Akira Muto, Yuki Iwasaki, Toshimichi Ikemura.
"tRNADB-CE: tRNA gene database well-timed in the era of big sequence data"
Frontiers in GENETICS, 5, 114, 2014. doi: 10.3389/fgene.2014.00114
Takashi Abe, Toshimichi Ikemura, Junichi Sugahara, Akio Kanai, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto and Hachiro Inokuchi
"tRNADB-CE 2011: tRNA gene database curated manually by experts"
Nucleic Acids Research, 39(Database isuue), D210-D213, 2011. doi: 10.1093/nar/gkq1007
Takashi Abe, Toshimichi Ikemura, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto and Hachiro Inokuchi
"tRNADB-CE: tRNA gene database curated manually by experts"
Nucleic Acids Research, 37(Database issue), D163-D168, 2009. doi:10.1093/nar/gkn692
Details of annotation strategy written in Japanese (click here
Data Version 11.0. Last update: 2018/01/09
BLASTN / Pattern Search
tRNA gene data download