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. 2004 Jan 2;32(1):11-6.
doi: 10.1093/nar/gkh152. Print 2004.

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

Dean Laslett  1 , Bjorn Canback
Affiliations

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

Dean Laslett et al. Nucleic Acids Res. .

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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Figures

Figure 1
Figure 1
Canonical tRNA cloverleaf secondary structure and numbering system. Diagram redrawn from Sprinzl et al. (12) with permission. Stem and loop descriptions have been added and the C-stem uppermost bond line has been removed to give a 5 bp C-stem, as in figure 4 of Eddy and Durbin (7).
Figure 2
Figure 2
Example output of the computer program ARAGORN from a search of eubacterial tRNA genes in the Sprinzl database (12).
See this image and copyright information in PMC

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