ArticleNucleic acids research2009
tRNADB-CE: tRNA gene database curated manually by experts.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 33 citations in OpenAlex.
- The Evolution of the First Code.Genes · 2026Review
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
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- tRNADB-CE: tRNA gene database well-timed in the era of big sequence data.Frontiers in genetics · 2014Review
- Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes.Nucleic acids research · 2013Article
- Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.Plant & cell physiology · 2013Article
- On ribosome load, codon bias and protein abundance.PloS one · 2012Article
- lncRNAdb: a reference database for long noncoding RNAs.Nucleic acids research · 2011Article
- tRNADB-CE 2011: tRNA gene database curated manually by experts.Nucleic acids research · 2011Article
- Genomic organization of eukaryotic tRNAs.BMC genomics · 2010Article
- Unique cost dynamics elucidate the role of frameshifting errors in promoting translational robustness.Genome biology and evolution · 2010Article
- Biogenesis of glutaminyl-mt tRNAGln in human mitochondria.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.Nucleic acids research · 2009Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 approximately 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.
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