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

      1 ,
      Nucleic Acids Research
      Oxford University Press (OUP)

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          Abstract

          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.

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          Author and article information

          Journal
          Nucleic Acids Research
          Oxford University Press (OUP)
          0305-1048
          1362-4962
          March 1997
          March 01 1997
          March 01 1997
          March 1997
          March 01 1997
          March 01 1997
          : 25
          : 5
          : 955-964
          Affiliations
          [1 ]Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA
          Article
          10.1093/nar/25.5.955
          146525
          9023104
          5490b00a-136d-42e4-bfab-e08774cf9fdd
          © 1997
          History

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