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

Nucleic Acids Res. 1997 Mar 1;25(5):955-64. doi: 10.1093/nar/25.5.955.


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.

MeSH terms

  • Animals
  • Databases, Factual
  • Evaluation Studies as Topic
  • Genome
  • Introns
  • RNA / genetics
  • RNA, Bacterial / analysis
  • RNA, Bacterial / genetics
  • RNA, Mitochondrial
  • RNA, Transfer / analysis
  • RNA, Transfer / genetics*
  • RNA, Transfer, Amino Acid-Specific / genetics
  • Software*


  • RNA, Bacterial
  • RNA, Mitochondrial
  • RNA, Transfer, Amino Acid-Specific
  • tRNA, selenocysteine-
  • RNA
  • RNA, Transfer