PredictRegulon: A web server for the prediction of the regulatory protein in binding sites and operons in prokaryote genomes

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Yellaboina, Sailu ^a   Seshadri, Jayashree ^a   Kumar, M Senthil ^a   Ranjan, Akash ^a  

^a CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

REGULATOR PROTEIN;

ACCESS TO INFORMATION; ARTICLE; BINDING SITE; CIS ISOMER; COMPUTER SYSTEM; CONTROLLED STUDY; DNA SEQUENCE; GENE CONTROL; HUMAN COMPUTER INTERACTION; INTERNET; NUCLEOTIDE SEQUENCE; OPERON; ORTHOLOGY; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROKARYOTE; PROTEIN BINDING; SEQUENCE ALIGNMENT; TRANS ISOMER;

5' FLANKING REGION; BACTERIAL PROTEINS; BINDING SITES; GENOME, BACTERIAL; INTERNET; MYCOBACTERIUM TUBERCULOSIS; OPERON; PROKARYOTIC CELLS; REGULATORY SEQUENCES, NUCLEIC ACID; REGULON; SEQUENCE ALIGNMENT; SERINE ENDOPEPTIDASES; SOFTWARE; TRANSCRIPTION FACTORS;

PROKARYOTA;

EID: 3242879355     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh364     Document Type: Article

References (12)

1. Salgado,H., Santos-Zavaleta,A., Gama-Castro,S., Millan-Zarate,D., Diaz-Peredo,E., Sanchez-Solano,F., Perez-Rueda,E., Bonavides-Martinez,C. and Collado-Vides,J. (2001) RegulonDB (Version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res., 29, 72-74.
2. Munch,R., Hiller,K., Barg,H., Heldt,D., Linz,S., Wingender,E. and Jahn,D. (2003) PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res., 31, 266-269.
3. Ishii,T., Yoshida,K., Terai,G., Fujita,Y. and Nakai,K. (2001) DBTBS: a database of Bacillus subtilis promoters and transcription factors. Nucleic Acids Res., 29, 278-280.
4. Shannon,C.E. (1948) A mathematical theory of communication. Bell Sys. Tech. J., 379-423 and 623-656.
5. Benos,P.V., Bulyk,M.L. and Stormo,G.D. (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res., 30, 4442-4451.
6. Ermolaeva,M.D., White,O. and Salzberg,S.L. (2001) Prediction of operons in microbial genomes. Nucleic Acids Res., 295, 1216-1221.
7. Salgado,H., Moreno-Hagelsieb,G., Smith,T.F. and Collado-Vides,J. (2000) Operons in Escherichia coli: genomic analyses and predictions Proc. Natl Acad. Sci., USA, 97, 6652-6657.
8. Strong,M., Mallick P., Pellegrini,M., Thompson,M.J. and Eisenberg,D. (2003) Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol., 4, R59.
9. Durbach,S.I., Andersen,S.J. and Mizrahi,V. (1997) SOS induction in mycobacteria: analysis of the DNA-binding activity of a LexA-like repressor and its role in DNA damage induction of the recA gene from MYcobacterium smegmatis. Mol. Microbiol., 26, 643-653.
10. Brooks,P.C., Movahedzadeh,F. and Davis,E.O. (2001) Identification of some DNA damage-inducible genes of Mycobacterium tuberculosis: apparent lack of correlation with LexA binding. J. Bacteriol., 183, 4459-4467.
11. Dullaghan,E.M.,Brooks,P.C. and Davis,E.O. (2002) The role of multiple SOS boxes upstream of the Mycobacterium tuberculosis lexA gene - identification of a novel DNA-damage-inducible gene. Microbiology, 148, 3609-3615.
12. Boshoff,H.I., Reed,M.B., Barry,C.E. and Mizrahi,V. (2003) DNAE2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis. Cell, 113, 183-193.