Database Description

General information of database
Database name	tRNADB-CE
Alternative name	-
DOI	10.18908/lsdba.nbdc00720-000
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
Contact address	Email:
Database classification	RNA sequence databases
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.
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).
License	CC BY-SA Detail
Background and funding	Name MEXT Integrated Database Project
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. External Links 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. External Links
Original website information
Database maintenance site	Bioinformatics Laboratory, Information Engineering, Niigata University
URL of the original website	http://trna.ie.niigata-u.ac.jp/
Operation start date	2008/7/1
Last update date	2012/7/23
URL of the portal site	http://biosciencedbc.jp/nbdc.cgi?lng=en
Whole data download	http://trna.ie.niigata-u.ac.jp/cgi-bin/trnadb/index.cgi
Referenced database	GENBANK/DDBJ/EBI
Entry list	Not available
Query search	Not available
Web services	Not available
URL of Web services	-
Need for user registration	Not available