tRNADB-CE
: tRNA gene database curated manually by experts
Takashi Abe1, Toshimichi Ikemura2, Junichi Sugahara3, Akio Kanai3, Yasuo Ohara2, Hiroshi Uehara2, Makoto Kinouchi4,
Shigehiko Kanaya5, Yuko Yamada2, Akira Muto6, Hachiro Inokuchi2
1. Niigata Univ., 2. Nagahama Inst. of Bio-Sci. and Tech., 3. Keio Univ., 4. Yamagata Univ., 5. NAIST, 6. Hirosaki Univ.
Introduction
The tRNA Gene DataBase Curated by Experts "tRNADB-CE" was constructed by analyzing 15,388 complete and 133,005 draft genomes of Bacteria and Archaea, 491 complete virus genomes, 2,886 complete phage genomes, 1,515 complete plasmid genomes, 2,325 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 780 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 14,580,858 tRNA genes in total 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
Review Article
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
Current version
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
Original version
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 13.0. Last update: 2020/09/28
Data List
| Data Type | Genomes | t RNA genes | |
| Prokaryote | Bacteria | 15126 | 958810 |
| Archaea | 262 | 12241 | |
| Draft-Bacteria | 132033 | 8508371 | |
| Draft-Archaea | 972 | 31051 | |
| Eukaryote | Plant | 2 | 1352 |
| Fungi | 10 | 2188 | |
| Virus | 491 | 974 | |
| Phage | 2886 | 13919 | |
| Plasmid | 1515 | 3852 | |
| Chloroplast | 2325 | 75248 | |
| Environmental sample (ENV) | 8120 | 4917980 | |
| ENV from Sequence Read Archive (SRA) | 87 | 54872 | |
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. |
Bioinformatics Laboratory, Information Engineering, Niigata University. | |