Affordable Access

Publisher Website

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

Authors
Type
Published Article
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Volume
44
Issue
D1
Pages
184–189
Identifiers
DOI: 10.1093/nar/gkv1309
Source
UCSC Bioinformatics biomedical-ucsc
License
Unknown

Abstract

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/.

Report this publication

Statistics

Seen <100 times