tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence

被引：9001

作者：

Lowe, TM ^{[1
]}

Eddy, SR ^{[1
]}

机构：

[1] WASHINGTON UNIV, SCH MED, DEPT GENET, ST LOUIS, MO 63110 USA

来源：

NUCLEIC ACIDS RESEARCH | 1997年 / 25卷 / 05期

关键词：

D O I：

10.1093/nar/25.5.955

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：955 / 964

页数：10