PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes

Bioinformatics

Volumn 20, Issue 5, 2004, Pages 629-635

  Lavigne, R ^a   Sun, W D ^a   Volckaert, Guido ^a  

^a LABORATORY OF GENE TECHNOLOGY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA; VIRUS PROTEIN;

ARTICLE; BACTERIOPHAGE; BACTERIOPHAGE LAMBDA; BACTERIOPHAGE T3; BACTERIOPHAGE T7; COMPUTER PREDICTION; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC REGULATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VIRUS GENOME;

UNIDENTIFIED BACTERIOPHAGE;

EID: 1842559901     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg456     Document Type: Article

References (20)

1. Brüssow,H. and Hendrix,R.W. (2002) Phage genomics: Small is beautiful. Cell, 108, 13-16.
2. Chen,Q.K., Hertz,G.Z. and Stormo,G.D. (1997) PromFD 1.0: A computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. Comput. Appl. Biosci., 13, 29-35.
3. d'Herelle,F. (1917) Sur un microbe antagoniste des bacilles dysentériques. CR Acad. Sci. Paris, 165, 373-375.
4. Dodson,M., Roberts,J., McMacken,R. and Echols,H. (1985) Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: Complexes with lambda O protein and with lambda O, lambda P, and Escherichia coli DnaB proteins. Proc. Natl Acad. Sci. USA, 82, 4678-4682.
5. Dunn,J.J. and Studier,F.W. (1983) Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol., 166, 477-535.
6. Dunn,J.J. and Studier,F.W. (1981) Nucleotide sequence from the genetic left end of bacteriophage T7 DNA to the beginning of gene 4. J. Mol. Biol., 148, 303-330.
7. Galas,D.J., Eggert,M. and Waterman,M.S. (1985) Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J. Mol. Biol., 186, 117-128.
8. Kaneko,J., Kimura,T., Narita,S., Tomita,T. and Kamio,Y. (1998) Complete nucleotide sequence and molecular characterization of the temperate staphylococcal bacteriophage phiPVL carrying Panton-Valentine leukocidin genes. Gene, 215, 57-67.
9. Krieg,P.A. and Melton,D.A. (1984) Functional messenger RNAs are produced by SP6 in vitro transcription of cloned cDNAs. Nucleic Acids Res., 12, 7057-7070.
10. Lavigne,R., Burkal'tseva,M.V., Robben,J., Sykilinda,N.N., Kurochkina,L.P., Grymponprez,B., Jonckx,B., Krylov,V.N., Mesyanzhinov,V.V. and Volckaert,G. (2003) The genome of bacteriophage φKMV, a T7-like virus infecting Pseudomonas aeruginosa. Virology, 312, 49-59.
11. Marsan,L. and Sagot,M.F. (2000) Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J. Comput. Biol., 7, 345-362.
12. Mesyanzhinov,V.V.,Robben,J., Grymonprez,B., Kostyuchenko,V.A., Burkal'tseva,M.V., Sykilinda,N.N., Krylov,V.N. and Volckaert,G. (2002) The genome of bacteriophage φKZ of Pseudomonas aeruginosa. J. Mol. Biol., 317, 1-19.
13. Miller,E.S., Kutter,E., Mosig,G., Arisaka,F., Kunisawa,T. and Ruger,W. (2003) Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev., 67, 86-156.
14. Pajunen,M.I., Elizondo,M.R., Skurnik,M., Kieleczawa,J. and Molineux,I.J. (2002) Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3. J. Mol. Biol., 319, 1115-1132.
15. Pajunen,M.I., Kiljunen,S.J., Soderholm,M.E. and Skurnik,M. (2001) Complete genomic sequence of the lytic bacteriophage φYeO3-12 of Yersinia enterocolitica serotype O:3. J. Bacteriol., 183, 1928-1937.
16. Pesole,G., Prunella,N., Liuni,S., Attimonelli,M. and Saccone,C. (1992) WORDUP: An efficient algorithm for discovering statistically significant patterns in DNA sequences. Nucleic Acids Res., 20, 2871-2875.
17. Rice,P., Longden,I. and Bleasby,A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
18. Stone,R. (2002) Bacteriophage therapy. Stalin's forgotten cure. Science, 298, 728-731.
19. Stormo,G.D. (1990) Consensus patterns in DNA. Meth. Enzymol., 183, 211-221.
20. van Helden,J., André,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.