GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

By Patricia P. Chan, Todd M. Lowe. Nucleic Acids Res., 2015

951 citations recorded by the source corpus.

Transfer RNAs represent the largest, most ubiquitous class of non-protein coding RNA genes found in all living organisms. The tRNAscan-SE search tool has become the de facto standard for annotating tRNA genes in genomes, and the Genomic tRNA Database (GtRNAdb) was created as a portal for interactive exploration of these gene predictions. Since its published description in 2009, the GtRNAdb has steadily grown in content, and remains the most commonly cited web-based source of tRNA gene information. In this update, we describe not only a major increase in the number of tRNA predictions (>367000) and genomes analyzed (>4370), but more importantly, the integration of new analytic and functional data to improve the quality and biological context of tRNA gene predictions. New information drawn from other sources includes tRNA modification data, epigenetic data, single nucleotide polymorphisms, gene expression and evolutionary conservation. A richer set of analytic data is also presented, including better tRNA functional prediction, non-canonical features, predicted structural impacts from sequence variants and minimum free energy structural predictions. Views of tRNA genes in genomic context are provided via direct links to the UCSC genome browsers. The database can be searched by sequence or gene features, and is available at http://gtrnadb.ucsc.edu/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/32ff427b49e30cb466eb19de72ba4f5fde0e8228

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In Molecular Biology

Citations in the corpus

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes (2016, methodology): “Transfer RNAs predicted using tRNAscan-SE are currently available for thousands of genomes in the GtRNAdb (2,3), yet the GtRNAdb is not designed for user-driven tRNA gene detection.”
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, background): “The majority of archaeal tRNA introns are located one nucleotide downstream of the anticodon (position 37/38), yet some have been found at seemingly random, ‘noncanonical’ positions in tRNA genes (5,36,68,92).”
RNAcentral: a hub of information for non-coding RNA sequences (2018, positive): “Following a major upgrade of the tRNAscan-SE software, Genomic tRNA Database (GtRNAdb) (21) now provides a much broader range of tRNA sequences, including tRNAs with possible introns.”
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases (2020, methodology): “RNA 2D STRUCTURE INTEGRATION Since 2017 RNAcentral has included 2D structure information starting with a tRNA dataset submitted by Genomic tRNA Database (GtRNAdb) (7).”
Genenames.org: the HGNC and VGNC resources in 2021 (2020, methodology): “Since September 2018, we have also named 60 microRNAs in collaboration with miRBase (27), 15 transfer RNAs in collaboration with GtRNAdb (28), and 8 variant small nuclear RNAs following consultation with our specialist advisor Dawn O’Reilly.”