tRNAscan-SE：用于改进基因组序列中转运RNA基因检测的程序。
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
作者信息
Lowe T M, Eddy S R
机构信息
Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA.
出版信息
Nucleic Acids Res. 1997 Mar 1;25(5):955-64. doi: 10.1093/nar/25.5.955.
Abstract
We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.
摘要
我们描述了一个名为tRNAscan-SE的程序，它能识别出DNA序列中99%至100%的转运RNA基因，同时每150亿碱基中产生的假阳性不到一个。两个先前描述的tRNA检测程序被用作快速的初步预过滤器，以识别候选tRNA，然后通过高度选择性的tRNA协方差模型对其进行分析。这项工作代表了RNA协方差模型的实际应用，RNA协方差模型是基于随机上下文无关文法的通用概率二级结构图谱。tRNAscan-SE的搜索速度约为每秒30000碱基对。tRNAscan-SE的其他扩展功能可检测异常的tRNA同源物，如硒代半胱氨酸tRNA、tRNA衍生的重复元件和tRNA假基因。
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