tRNADB-CE
: tRNA gene database curated manually by experts
Takashi Abe1, Toshimichi Ikemura1, Junichi Sugahara2, Akio Kanai2, Yasuo Ohara1, Hiroshi Uehara1, Makoto Kinouchi3,
Shigehiko Kanaya4, Yuko Yamada1, Akira Muto5, Hachiro Inokuchi1
1. Nagahama Inst. of Bio-Sci. and Tech., 2. Keio Univ., 3. Yamagata Univ., 4. NAIST, 5. Hirosaki Univ.
Introduction
The tRNA Gene DataBase Curated by Experts “tRNADB-CE” was constructed by analyzing 740 complete and 616 draft genomes of Bacteria and Archaea, 151 complete virus genomes and approximately 17 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 and tRNAfinder, 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 were included.The 172,073 tRNA genes in total (42,575, 33,383, 961 and 95,154 genes from complete genomes, draft genomes, virus 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.
Reference
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, 2009, 37(Database issue), D163-D168, doi:10.1093/nar/gkn692
Details of annotation strategy written in Japanese (click here).
Data Version 3.0. Last update: 2009/08/18
Data List
| Data Type | Genomes | tRNA genes | |
| Complete genome | Bacteria | 693 | 40435 |
| Archaea | 47 | 2140 | |
| Draft genome (Whole Genome Shotgun sequence data, WGS) | 616 | 33383 | |
| Environmental sample (ENV) | 100 | 95154 | |
| Virus | 31 | 151 | |
| Phage | 120 | 810 | |
Keyword Search
BLASTN / Pattern Search
tRNA gene data download
 | tRNADB-CE was supported by Integrated Database Project from the Ministry of Education, Culture, Sports, Science and Technology, Japan. |
Nagahama Institute of Bio-Science and Technology | |