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

Nucleic Acids Research

Volumn 32, Issue 1, 2004, Pages 11-16

  Laslett, Dean ^b   Canback, Bjorn ^a  

^a LUND UNIVERSITY   (Sweden)

^b MURDOCH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL RNA; MITOCHONDRIAL RNA; TRANSFER RNA; BACTERIAL RNA; TMRNA;

ARTICLE; BASE PAIRING; CHLOROPLAST; COMPUTER PROGRAM; CONTROLLED STUDY; EUBACTERIUM; EUKARYOTE; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC DATABASE; GREEN ALGA; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; RNA GENE; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY; ALGORITHM; BIOLOGY; CHEMISTRY; CONFORMATION; GENETICS; GENOMICS; INTERNET; METHODOLOGY; MOLECULAR GENETICS;

ALGAE; ARCHAEA; BACTERIA (MICROORGANISMS); CHLOROPHYTA; EUKARYOTA; NEGIBACTERIA;

ALGORITHMS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; GENOMICS; INTERNET; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, BACTERIAL; RNA, TRANSFER; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 1242297827     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh152     Document Type: Article

References (13)

1. Kim,S.H., Suddath,F.L., Quigley,G.J., McPherson,A., Sussman,J.L., Wang,A.H.J., Seeman,N.C. and Rich,A. (1974) Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science, 185, 435-440.
2. Sharp,S.J., Schaak,J., Cooley,L., Burke,D.J. and Söll,D. (1985) Structure and transcription of eukaryotic tRNA genes, CRC Crit. Rev. Biochem., 19, 107-144.
3. Fichant,G.A. and Burks,C. (1991) Identifying potential tRNA genes in genomic DNA sequences. J. Mol. Biol., 220, 659-671.
4. Muto,A., Ushida,C. and Himeno,H. (1998) A bacterial RNA that functions as both a tRNA and an mRNA Trends Biochem. Sci., 23, 25-29.
5. Keiler,K.C., Shapiro,L. and Williams,K.P. (2000) tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: a two-piece tmRNA functions in Caulobacter. Proc. Natl Acad. Sci. USA, 97, 7778-7783.
6. Gueneau de Novoa,P. and Williams,K.P. (2004) The tmRNA Website: reductive evolution of tmRNA in plastids and other endosymbionts. Nucleic Acids Res., 32, D104-D108.
7. Eddy,S.R. and Durbin,R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079-2088.
8. Pavesi,A., Conterio,F., Bolchi,A., Dieci,G. and Ottonello,S. (1994) Identification of new eukaryotic tRNA genes in generate DNA databases by a multistep weight matrix analysis of transcription control regions. Nucleic Acids Res., 22, 1247-1256.
9. Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
10. Tsui,V., Macke,T. and Case,D.A. (2003) A novel method for finding tRNA genes. RNA, 9, 507-517.
11. Laslett,D., Canback,B. and Andersson,S. (2002) BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences. Nucleic Acids Res., 30, 3449-3453.
12. Sprinzl,M., Horn,C., Brown,M., Ioudovitch,A. and Steinberg,S. (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 26, 148-153.
13. Williams,K.P. (2002) The tmRNA Website: invasion by an intron. Nucleic Acids Res., 30, 179-182.