GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes.
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes.
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DOI：
10.1093/nar/gkv1309
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Lowe TM
中科院分区：
文献类型：
--
作者：
Chan PP;Lowe TM
转移RNA代表了在所有生物体中发现的最大、最普遍的一类非蛋白质编码RNA基因。tRNAscan-SE搜索工具已成为注释基因组中tRNA基因的事实上的标准，而基因组tRNA数据库（GtRNAdb）被创建为交互式探索这些基因预测的门户。自2009年发表描述以来，GtRNAdb的内容稳步增长，并且仍然是最常被引用的基于网络的tRNA基因信息来源。在这次更新中，我们不仅描述了tRNA预测（>367000）和分析的基因组（>4370）数量的大幅增加，更重要的是，整合了新的分析和功能数据，以提高tRNA基因预测的质量和生物学背景。从其他来源获得的新信息包括tRNA修饰数据、表观遗传数据、单核苷酸多态性、基因表达和进化保护。还提供了更丰富的分析数据集，包括更好的tRNA功能预测，非典型特征，预测序列变体的结构影响和最小自由能结构预测。通过UCSC基因组浏览器的直接链接，提供了基因组背景下的tRNA基因视图。该数据库可以通过序列或基因特征进行搜索，可在http://gtrnadb.ucsc.edu/上获得。
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/.