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

Laslett, D and Canbäck, Björn LU (2004) In Nucleic Acids Research 32(1). p.11-16
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... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Nucleic Acids Research
volume
32
issue
1
pages
11 - 16
publisher
Oxford University Press
external identifiers
  • wos:000188988700016
  • pmid:14704338
  • scopus:1242297827
ISSN
1362-4962
DOI
10.1093/nar/gkh152
language
English
LU publication?
yes
id
5062e5f3-be0a-464f-ba69-f62eddc14f57 (old id 135675)
alternative location
http://nar.oupjournals.org/cgi/content/abstract/32/1/11
date added to LUP
2007-06-29 11:53:14
date last changed
2017-12-10 03:56:12
@article{5062e5f3-be0a-464f-ba69-f62eddc14f57,
  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.},
  author       = {Laslett, D and Canbäck, Björn},
  issn         = {1362-4962},
  language     = {eng},
  number       = {1},
  pages        = {11--16},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences},
  url          = {http://dx.doi.org/10.1093/nar/gkh152},
  volume       = {32},
  year         = {2004},
}