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

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Author

  • D Laslett
  • Björn Canbäck

Summary, in English

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.

Publishing year

2004

Language

English

Pages

11-16

Publication/Series

Nucleic Acids Research

Volume

32

Issue

1

Document type

Journal article

Publisher

Oxford University Press

Topic

  • Biological Sciences

Status

Published

Research group

  • Microbial Ecology

ISBN/ISSN/Other

  • ISSN: 1362-4962