ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/135675
- author
- Laslett, D and Canbäck, Björn LU
- organization
- publishing date
- 2004
- 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
- pmid:14704338
- 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
- 2016-04-01 12:37:04
- date last changed
- 2024-05-08 20:03:07
@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}}, doi = {{10.1093/nar/gkh152}}, volume = {{32}}, year = {{2004}}, }