Introduction

    The tRNA Gene DataBase Curated by Experts "tRNADB-CE" was constructed by analyzing 4,287 complete and 47,370 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 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 2,980,064 tRNA genes in total (252,946, 2,558,137, 4601, 3534, 4137 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.

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 10.0. Last update: 2016/11/17


Data List

Data TypeGenomest RNA genes
Prokaryote Bacteria 4237 250737
Archaea 50 2209
Draft 47370 2558137
Eukaryote Plant 2 1346
Fungi 10 2188
Virus 31 151
Phage 845 4450
Chloroplast 121 4137
Environmental sample (ENV) 134 101837
ENV from Sequence Read Archive (SRA) 87 54872

Keyword Search

Keyword: and or  (Multiple keywords should be separated with a space.)
Targets: Species name Amino Acid Anticodon Sequence ID Genome ID
Data Types: Bacteria Archaea Draft Plant Fungi Virus Phage Chloroplast ENV SRA
>>Advanced Search


BLASTN / Pattern Search

Query Sequence:

MultiFASTA file upload (BLASTN only)
Search Type:
BLASTN
      e-value
      Number of sequences to show(max=500)
      Advanced BLAST option
Pattern
      Acceptor-stem D-stem D-loop Anticodon-stem
      Anticodon-loop Variable-loop T-stem T-loop
Data Types:
Bacteria Archaea Draft Plant Fungi Virus Phage Chloroplast ENV SRA
>>Advanced Pattern Search

tRNA gene data download

File Type:
FASTA
Tab delimited data
Data Types:
Bacteria Archaea Draft Plant Fungi Virus Phage Chloroplast ENV SRA
Target:
The reliable tRNA genes
All candidate tRNA genes



Identical Sequence Group

Data TypeGenomesSequence groups
Prokaryote Bacteria 51118 131660
Archaea 50 1752
Plant Plant 2 438
Fungi 10 511
Virus 31 97
Phage 767 2128
Chloroplast 121 1731
ENV 134 35616
ENV from Sequence Read Archive (SRA) 87 26188

Identical Sequence Group (ENV vs Prokaryote Genome)

100% (Identical)  |  97% (2-nt difference)  |  95% (3-nt difference)


Identical Sequence Group (SRA vs Prokaryote Genome)

100% (Identical)  |  97% (2-nt difference)  |  95% (3-nt difference)



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