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

Transfer RNAs represent the largest, most ubiqui-tous class of non-protein coding RNA genes found in all living organisms. The tRNAscan-SE search tool has become the de facto standard for anno-tating tRNA genes in genomes, and the Genomic tRNA Database (GtRNAdb) was created as a por-tal for interactive exploration of these gene predic-tions. 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 pre-dictions (>367000) and genomes analyzed (>4370), but more importantly, the integration of new analytic and functional data to improve the quality and bi-ological context of tRNA gene predictions. New in-formation 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 predic-tion, non-canonical features, predicted structural im-pacts from sequence variants and minimum free en-ergy 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 avail-able a