tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
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DOI：
10.1093/nar/25.5.955
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发表时间：
1997-03-01
影响因子：
14.9
通讯作者：
Eddy, SR
中科院分区：
文献类型：
--
作者：
Lowe, TM;Eddy, SR
我们描述了一个程序，tRNAscan-SE，它可以识别DNA序列中99% -100%的转移RNA基因，同时每15千兆酶产生少于一个假阳性。两个先前描述的tRNA检测程序被用作快速，第一遍预过滤器来识别候选tRNA，然后通过高选择性tRNA协方差模型进行分析。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语法的一般概率二级结构剖面。tRNAscan-SE的搜索速度接近于30000 bp/s。tRNAscan-SE的附加扩展可检测异常的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。
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 similar to 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.