Nucleic Acids Research Advance Access originally published online on October 8, 2008
Nucleic Acids Research 2009 37(Database issue):D163-D168; doi:10.1093/nar/gkn692
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2009, Vol. 37, Database issue D163-D168
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
tRNADB-CE: tRNA gene database curated manually by experts
1Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 2Department of Bio-System Engineering, Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, 3Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara and 4Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
*To whom correspondence should be addressed. Tel: +81 749 64 8100; Fax: +81 749 64 8140; Email: takaabe{at}nagahama-i-bio.ac.jp
Received August 8, 2008. Revised September 22, 2008. Accepted September 25, 2008.
We constructed a new large-scale database of tRNA genes by analyzing 534 complete genomes of prokaryotes and 394 draft genomes in WGS (Whole Genome Shotgun) division in DDBJ/EMBL/GenBank and approximately 6.2 million DNA fragment sequences obtained from metagenomic analyses. This exhaustive search for tRNA genes was performed by running three computer programs to enhance completeness and accuracy of the prediction. Discordances of assignment among three programs were found for 
4% of the total of tRNA gene candidates obtained from these prokaryote genomes analyzed. The discordant cases were manually checked by experts in the tRNA experimental field. In total, 144 061 tRNA genes were registered in the database ‘tRNADB-CE’, and the number of the genes was more than four times of that of the genes previously reported by the database from analyses of complete genomes with tRNAscan-SE program. The tRNADB-CE allows for browsing sequence information, cloverleaf structures and results of similarity searches among all tRNA genes. For each of the complete genomes, the number of tRNA genes for individual anticodons and the codon usage frequency in all protein genes and the positioning of individual tRNA genes in each genome can be browsed. tRNADB-CE can be accessed freely at http://trna.nagahama-i-bio.ac.jp.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Nagao, T. Suzuki, T. Katoh, Y. Sakaguchi, and T. Suzuki Biogenesis of glutaminyl-mt tRNAGln in human mitochondria PNAS, September 22, 2009; 106(38): 16209 - 16214. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Y. Galperin and G. R. Cochrane Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009 Nucleic Acids Res., January 1, 2009; 37(suppl_1): D1 - D4. [Abstract] [Full Text] [PDF]
|
|