tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

作者：Todd M. Lowe, Sean R. Eddy · 发表于：Nucleic Acids Research · 年份：1997 · DOI：10.1093/nar/25.5.955 · 被引用次数：11286 · 研究领域：RNA and protein synthesis mechanisms、Genomics and Phylogenetic Studies、RNA modifications and cancer

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.