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tRNADB-CE

Database Description

General information of database

info Database name tRNADB-CE
info Alternative name -
info Creator 
Creator Name:
Takashi Abe*
Creator Affiliation:
Graduate School of Science and Technology, Niigata University
Creator Name:
Toshimichi Ikemura
Creator Affiliation:
Laboratory of biomolecular information, Nagahama Institute of Bio-Science and Technology
Creator Name:
Junichi Sugawara
Creator Affiliation:
Keio University
Creator Name:
Akio Kanai
Creator Affiliation:
Keio University
Creator Name:
Yasuo Ohara
Creator Affiliation:
Laboratory of biomolecular information, Nagahama Institute of Bio-Science and Technology
Creator Name:
Hiroshi Uehara
Creator Affiliation:
Laboratory of biomolecular information, Nagahama Institute of Bio-Science and Technology
Creator Name:
Makoto Kinouchi
Creator Affiliation:
Yamagata University
Creator Name:
Shigehiko Kanaya
Creator Affiliation:
Nara Institute of Science and Technology
Creator Name:
Yuko Yamada
Creator Affiliation:
Laboratory of biomolecular information, Nagahama Institute of Bio-Science and Technology
Creator Name:
Akira Muto
Creator Affiliation:
Hirosaki University
Creator Name:
Hachiro Inokuchi
Creator Affiliation:
Laboratory of biomolecular information, Nagahama Institute of Bio-Science and Technology
info Contact address 

Email: trnadb-ce_ad

info Database classification RNA sequence databases
info Organism 

-

info Database description 

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 sequenced prokaryote, eukaryote and virus genomes and envrironmental DNA sequences, and then the experts manually check those cases in which different results are generated by program.

info Features and manner of utilization of database 

- The database was constructed by performing a comprehensive search of tRNA genes on 1625 full-length genomes and 2993 draft genomes of bacteria and Archaea, 151 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and about 230 million environmental DNA sequences.
- Three prediction programs (tRNAScan-SE, Aragorn and tRNA finder) are used together to search tRNA genes. If the prediction results do not match, curation is carried out by experts.
- The relationship between the codon usage frequency and the number of tRNA genes can be browsed for each species to search the codon recognized by major isoaccepting tRNA (optimal codon) or minor tRNA (nonoptimal codon).

info Background and funding 

MEXT Integrated Database Project

info Reference(s) 
Article title:
tRNADB-CE: tRNA gene database curated manually by experts.
Author name(s):
Abe T, Ikemura T, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H.
Journal:
Nucleic Acids Res. 2009 Jan;37(Database issue):D163-8.
Pubmed ID:
18842632
Article title:
tRNADB-CE 2011: tRNA gene database curated manually by experts.
Author name(s):
Abe T, Ikemura T, Sugahara J, Kanai A, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H.
Journal:
Nucleic Acids Res. 2011 Jan;39(Database issue):D210-3.
Pubmed ID:
21071414

Original website information

info Database maintenance site 

info URL of the original website 
info Operation start date 2008/7/1
info Last update date 2012/7/23
info URL of the portal site http://biosciencedbc.jp/nbdc.cgi?lng=en
info Whole data download http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/index.cgi
info Referenced database 

GENBANK/DDBJ/EBI

info Entry list Available
info Query search Available
info Web services Not available
info URL of Web services 

-

info Need for user registration -