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

Author:
  • D Laslett
  • Björn Canbäck
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

Abstract 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.

Keywords

  • Biological Sciences

Other

Published
  • Microbial Ecology
  • ISSN: 1362-4962
Björn Canbäck
E-mail: bjorn [dot] canback [at] biol [dot] lu [dot] se

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Molecular Cell Biology

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