Alpha 2.0
Login Register
» Articles » PMID: 14704338

ARAGORN, a Program to Detect TRNA Genes and TmRNA Genes in Nucleotide Sequences

Overview
Journal Nucleic Acids Res
Publisher Oxford University Press
Specialty Biochemistry
Date 2004 Jan 6
PMID 14704338
Citations 1638
Authors
Dean Laslett
Bjorn Canback
Affiliations
Soon will be listed here.
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.

Citing Articles

The Complete Genome Sequences of Bacteriophages ASegato, DejaVu, Judebell, and RicoCaldo isolated using .

Logan R, Biratu M, Busila M, Busto I, Caldwell N, Chestnut P MicroPubl Biol. 2025; 2025.

PMID: 40052136 PMC: 11883469. DOI: 10.17912/micropub.biology.001443.

Genome Sequence of Mycobacterium Phage Guppsters.

Alley E, Hill L, Houglum M, Lamppa M, Pack K, Pageau H MicroPubl Biol. 2025; 2025.

PMID: 40041766 PMC: 11877149. DOI: 10.17912/micropub.biology.001450.

Isolation and characterization of fMGyn-Pae01, a phiKZ-like jumbo phage infecting Pseudomonas aeruginosa.

Ranta K, Skurnik M, Kiljunen S Virol J. 2025; 22(1):55.

PMID: 40033410 PMC: 11877940. DOI: 10.1186/s12985-025-02679-w.

Genome Sequences of three CT cluster Bacteriophages isolated in Durham, North Carolina on .

Simmons K, Lambert A, Loekken M, Schreiner L, Copley C, Murthy T MicroPubl Biol. 2025; 2025.

PMID: 40027522 PMC: 11871531. DOI: 10.17912/micropub.biology.001487.

Transcriptomic analysis of Virescentia guangxiensis (Rhodophyta: Batrachospermales) revealed differential expression of genes in gametophyte and chantransia life phases.

Guo W, Nan F, Liu X, Liu Q, Feng J, Xie S BMC Genomics. 2025; 26(1):202.

PMID: 40016669 PMC: 11869606. DOI: 10.1186/s12864-025-11396-1.

References
1.
Pavesi A, CONTERIO F, Bolchi A, Dieci G, Ottonello S . Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions. Nucleic Acids Res. 1994; 22(7):1247-56. PMC: 523650. DOI: 10.1093/nar/22.7.1247. View
2.
Eddy S, Durbin R . RNA sequence analysis using covariance models. Nucleic Acids Res. 1994; 22(11):2079-88. PMC: 308124. DOI: 10.1093/nar/22.11.2079. View
3.
Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View
4.
Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S . Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1998; 26(1):148-53. PMC: 147216. DOI: 10.1093/nar/26.1.148. View
5.
Muto A, Ushida C, Himeno H . A bacterial RNA that functions as both a tRNA and an mRNA. Trends Biochem Sci. 1998; 23(1):25-9. DOI: 10.1016/s0968-0004(97)01159-6. View