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Citation
Chan, P.P., Lowe, T.M. (2016). GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes.  Nucleic Acids Res. 44(D1): D184--D189.
FlyBase ID
FBrf0248860
Publication Type
Research paper
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/.

PubMed ID
PubMed Central ID
PMC4702915 (PMC) (EuropePMC)
Related Publication(s)
Website

tRNAscan-SE analysis of the Drosophila melanogaster genome.
Lowe, 2002, tRNAscan-SE analysis of the Drosophila melanogaster genome. [FBrf0145624]

Associated Information
Comments

Curated data from tRNAscan-SE analysis of the Drosophila melanogaster genome (FBrf0145624).

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Other Information
Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Nucleic Acids Res.
    Title
    Nucleic Acids Research
    Publication Year
    1974-
    ISBN/ISSN
    0305-1048
    Data From Reference
    Genes (288)
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