GtRNAdb: a database of transfer RNA genes detected in genomic sequence

By Patricia P. Chan, Todd M. Lowe. Nucleic Acids Res., 2008

921 citations recorded by the source corpus.

Transfer RNAs (tRNAs) represent the single largest, best-understood class of non-protein coding RNA genes found in all living organisms. By far, the major source of new tRNAs is computational identification of genes within newly sequenced genomes. To organize the rapidly growing collection and enable systematic analyses, we created the Genomic tRNA Database (GtRNAdb), currently including over 74 000 tRNA genes predicted from 740 species. The web resource provides overview statistics of tRNA genes within each analyzed genome, including information by isotype and genetic locus, easily downloadable primary sequences, graphical secondary structures and multiple sequence alignments. Direct links for each gene to UCSC eukaryotic and microbial genome browsers provide graphical display of tRNA genes in the context of all other local genetic information. The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group. The database is publicly available at http://gtrnadb.ucsc.edu.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/988c4410cfa619985b149e13c9ba6be8f68115df

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Citations in the corpus

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA (2012, methodology): “Sequenced read mapping and analysis Sequenced reads were mapped against reference sequences consisting of all known human transcripts from the Ensembl v61 database (mRNA, rRNA, tRNA, mitochondrial RNA and all non-coding RNA) (41), predicted and known tRNA sequences obtained from the GtRNAdb (42) and”
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation (2014, methodology): “The filtering step used the tRNA from the Genomic tRNA database (Chan & Lowe, 2009) and Mt_rRNA, Mt_tRNA, rRNA, snoRNA, snRNA from Ensembl r73 non-coding RNAs.”
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes (2015, background): “This constitutes a more than 4x increase from the original description of the database (14).”
tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes (2016, methodology): “Accordingly, we plan to produce a tRNA gene set ‘completeness’ report using phylogenetic patterns of tRNA set composition observed across all genomes represented in the GtRNAdb.”
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, background): “tRNA genes predicted using tRNAscan-SE are also available in the Genomic tRNA Database (GtRNAdb) (4,5) for thousands of genomes, enabling the research community to browse high-quality tRNA collections across all three domains of life.”
Repbase Update, a database of repetitive elements in eukaryotic genomes (2015, background): “…and some integrated viral sequences — but these types of sequences are not as thoroughly collected as in other dedicated databases, such as SILVA ribosomal RNA gene database [11], 5S ribosomal RNA database [12], GtRNAdb [13], and “ paleovirology ” (http://bioinformatics.cvr.ac.uk/paleovirology/).”
Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system (2015, methodology): “These PTGs were constructed with a 77-bp long pre-tRNA gene, which recognizes the GGC codon and is widely present among various genomes (25).”