ReviewFrontiers in genetics2014
tRNADB-CE: tRNA gene database well-timed in the era of big sequence data.
Review in Frontiers in genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 54 citations in OpenAlex.
- Article
- GIPSy2: high-performance and scalable genomic island prediction software.Scientific reports · 2026Article
- Genomic analysis of prophages from Burkholderia gladioli exposes extensive genetic diversity.BMC genomics · 2026Article
- The Evolution of the First Code.Genes · 2026Review
- Review
- Molecular basis of human nuclear and mitochondrial tRNA 3' processing.Nature structural & molecular biology · 2025Article
- A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis.Nature chemical biology · 2025Article
- Profiling of Known and Novel microRNAs in an Oleaginous Crop Native to the Amazon Basin, Sacha Inchi (Genes · 2025Article
- Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids.Chemical reviews · 2024Review
- Article
- The tRNA identity landscape for aminoacylation and beyond.Nucleic acids research · 2023Review
- tatDB: a database of Ago1-mediated targets of transfer RNA fragments.Nucleic acids research · 2023Article
- Role of a cryptic tRNA gene operon in survival under translational stress.Nucleic acids research · 2021Article
- Accurate characterization ofRNA biology · 2021Article
- Diversity of tRNA Clusters in the Chloroviruses.Viruses · 2020Article
- Inferring targeting modes of Argonaute-loaded tRNA fragments.RNA biology · 2020Article
- Information theory unveils the evolution of tRNA identity elements in the three domains of life.Theory in biosciences = Theorie in den Biowissenschaften · 2020Article
- New Insights into the Relationship between tRNA Processing and Polyadenylation in Escherichia coli.Trends in genetics : TIG · 2019Review
- GlobalViruses · 2019Article
- Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The tRNA gene data base curated by experts "tRNADB-CE" (http://trna.ie.niigata-u.ac.jp) was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses', 121 chloroplasts', and 12 eukaryotes' genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group (ISG) can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that batch-learning self-organizing-map with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.