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      ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.

      1 ,
      Nucleic acids research
      Oxford University Press (OUP)

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          Abstract

          A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the 'green' algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.

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          Author and article information

          Journal
          Nucleic Acids Res
          Nucleic acids research
          Oxford University Press (OUP)
          1362-4962
          0305-1048
          2004
          : 32
          : 1
          Affiliations
          [1 ] Murdoch University, Perth, Western Australia, Australia.
          Article
          32/1/11
          10.1093/nar/gkh152
          373265
          14704338
          1b83fd2a-83b0-4993-9d85-2f2e36155810
          History

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