Introduction

    The tRNA Gene DataBase Curated by Experts "tRNADB-CE" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 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 287,103 tRNA genes in total (53936, 70080, 961, 3534, 4137 and 154455 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
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 4.0. Last update: 2010/06/29


Data List

Data TypeGenomestRNA genes
Prokaryote Bacteria 880 51796
Archaea 47 2140
Draft 1301 70080
Eukaryote Plant 2 1346
Fungi 10 2188
Virus 31 151
Phage 140 810
Chloroplast 121 4137
Environmental sample (ENV) 123 99583
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
Plokaryote Bacteria 2181 27939
Archaea 47 1690
Plant Plant 2 431
Fungi 10 510
Virus 31 97
Phage 140 484
Chloroplast 121 1677
ENV 123 34200
ENV from Sequence Read Archive (SRA) 87 25928

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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