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

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.

Pubmed ID: 9023104


  • Lowe TM
  • Eddy SR


Nucleic acids research

Publication Data

March 1, 1997

Associated Grants


Mesh Terms

  • Animals
  • Databases, Factual
  • Evaluation Studies as Topic
  • Genome
  • Introns
  • RNA
  • RNA, Bacterial
  • RNA, Transfer
  • RNA, Transfer, Amino Acid-Specific
  • Software