tRNADB-CE

2014/08/25

WebSite: http://trna.ie.niigata-u.ac.jp/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/trnadb_ce

This is the most accurate tRNA gene database curated manually by experts in the world. This database is the outcome of the model project to utilize the expertise of elderly researchers and to pass it down to the next generation, which was carried out at Nagahama Institute of Bio-Science and Technology. Specifically, the existing multiple tRNA gene search programs are used for automatic search of tRNA gene from almost all sequenced prokaryote genomes, and then the experts manually check those cases in which different results are generated by program.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. tRNA sequence data, annotation data and curation data
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "tRNADB-CE" data.
File README_e.html(English)
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2.2 tRNA sequence data, annotation data and curation data

Data name tRNA sequence data, annotation data and curation data
Description of data contents

Data of tRNA search results and curation data. Three prediction programs (tRNAScan-SE, Aragorn and tRNA finder) were used together to search tRNA genes. If the prediction results did not match, curation was carried out by experts.
The following three types of determinations are used for determining the results.
- reliable tRNA gene　("circle" mark at the original website.)
- ambiguous case　("triangle" mark at the original website.)
- not tRNA gene　("x" mark at the original website.)

The data are classified into nine types as follows according to sources.
- Prokaryotic complete genome: 95,512 entries.
- Prokaryotic draft genome (WGS): 196,032 entries.
- Plant: 1,608 entries.
- Fungus: 2,773 entries.
- Virus: 151 entries.
- Phage: 962 entries.
- Chloroplast: 4,376 entries.
- Environmental sample (ENV) from GenBank: 101,837 entries.
- Environmental sample (ENV) from Sequence Read Archive: 54,872 entries.

The number of data is 458,123 in total. The data are given in a CSV format text file.

File trnadb_ce.zip (22.7 MB)
Data items are the following:
Data item Description
Data type Types of acquired data. Classified into nine types including "Prokaryotic complete genome", "Prokaryotic draft genome (WGS)", "Plant", "Fungus", "Virus", "Phage", "Chloroplast", "Environmental sample (ENV) from GenBank" and "Environmental sample (ENV) from Sequence Read Archive".
Sequence ID Sequence ID
Genome ID Genome ID (Genome ID of DDBJ GIB is used.)
Phylum/Class Taxon name
Species Species name
Start position tRNA gene start position on the genome
End position tRNA gene end position on the genome
Direction Direction of tRNA gene on the genome
Amino Acid Amino acid type
Anticodon Anticodon
1st Intron start position Start position of first intron
1st Intron end position End position of first intron
Seq tRNA sequence
Upstream seq. tRNA gene upstream sequence (10 bps)
tRNA1-7 1st to 7th nucleotides in the clover-leaf secondary structures (*1) of tRNA gene
tRNA8-9 8th to 9th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA10-13 10th to 13th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA14-21 14th to 21st nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA22-25 22nd to 25th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA26 26th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA27-31 27th to 31st nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA32-38 32nd to 38th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA39-43 39th to 43rd nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA44-48 44th to 48th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA49-53 49th to 53rd nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA54-60 54th to 60th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA61-65 61st to 65th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA66-72 66th to 72nd nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA73-76 73rd to 76th nucleotides in the clover-leaf secondary structures of tRNA gene
Downstream seq. tRNA gene downstream sequence (10 bps)
1st Intron seq. First intron sequence
2nd Intron start position Start position of second intron
2nd Intron end position End position of second intron
2st Intron seq. Second intron sequence
Decision from Dr. Muto Determination 1 (Dr. Muto)
Decision from Dr. Inokuchi Determination 2 (Dr. Inokuchi)
Decision from Dr. Yamada Determination 3 (Dr. Yamada)
Comment of Dr. Muto Comment 1 (Dr. Muto)
Comment of Dr. Inokuchi Comment 2 (Dr. Inokuchi)
Comment of Dr. Yamada Comment 3 (Dr. Yamada)
Final decision Final Determination
Comments Comment
Original database Genome sequence source information

*1Registered for each common position on the clover-leaf secondary structure of tRNA gene. (For common position, see http://trna.ie.niigata-u.ac.jp/trnadb/tRNA_structure.jpg.)

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3. License

Last updated : 2011/08/25

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

Creative Commons License
The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "tRNADB-CE, © Nagahama Institute of Bio-Science and Technology licensed under CC Attribution-Share Alike 2.1 Japan".

The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other derivative works based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
  2. You must distribute any derivative work based on part or whole of the data from this database under the license.
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

Email: trnadbce[at]gmail[dot]com

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4. Update History

Date Update contents
2014/08/25 "Contact address", "Database maintenance site", "URL of the original website" and "Whole data download" are changed.
2012/07/23 - Data Updated
The data is updated to the latest version which is equivalent to the data version 6.1 of the original database.
Listed entries of tRNA genes are increased from 172,143 to 458,123.
The following list is the number of species used for the analysis.
  • Bacteria: 1578
  • Archaea: 47
  • Prokaryotic draft genome (WGS): 2993
  • Eukaryote (Plant and Fungus): 12
  • Virus: 151
  • Chloroplast: 121
  • Environmental sample (ENV) from GenBank: 134
  • Environmental sample (ENV) from Sequence Read Archive: 87
2011/08/25 "License" is updated.
2010/03/29 tRNADB-CE English archive site is opened.
1996/12 tRNADB-CE(http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/index.cgi) is released.
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5. Literature

Abe T, Ikemura T, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H.
tRNADB-CE: tRNA gene database curated manually by experts.
Nucleic Acids Res. 2009 Jan;37(Database issue):D163-8.
PMID:18842632

6. Contact address

When you have any question about "tRNADB-CE", contact the following:

Email: trnadbce[at]gmail[dot]com

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