YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3586-3588

  Sinha, Saurabh ^b   Tompa, Martin ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; COMPUTER PROGRAM; DNA BINDING MOTIF; GENE CONTROL; INTERNET; PRIORITY JOURNAL; PROTEIN DNA BINDING; STATISTICAL PARAMETERS; ALGORITHM; COMPUTER INTERFACE; DNA SEQUENCE; GENETICS; METABOLISM; METHODOLOGY; MYCOBACTERIUM TUBERCULOSIS; PROMOTER REGION; REGULATORY SEQUENCE; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS;

ALGORITHMS; BINDING SITES; DATA INTERPRETATION, STATISTICAL; INTERNET; MYCOBACTERIUM TUBERCULOSIS; PROMOTER REGIONS (GENETICS); REGULATORY SEQUENCES, NUCLEIC ACID; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 0042905768     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg618     Document Type: Article

References (9)

1. Bailey,T.L. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning, 21, 51-80.
2. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
3. Roth,F.P., Hughes,J.D., Estep,P.W. and Church,G.M. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol., 16, 939-945.
4. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
5. Sinha,S. and Tompa,M. (2002) Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res., 30, 5549-5560.
6. Sinha,S. and Tompa,M. (2000) A statistical method for finding transcription factor binding sites. In Bourne,P., Gribskov,M., Altman,R., Jensen,N., Hope,D., Lengauer,T., Mitchell,J., Scheeff,E., Smith,C., Strarde,S., and Weissig,H. (eds), Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, CA, pp. 344-354.
7. Park,H.-D., Guinn,K., Harrell,M.I., Liao,R., Voskull,M.I., Tompa,M., Schoolnik,G.K. and Sherman,D.R. (2003) Rv3133c/dosR is a transcription factor that mediates the hypoxic response of M. tuberculosis. Mol. Microbiol., 48, 833-843.
8. Sinha,S. and Tompa,M. (2003) Performance comparison of algorithms for finding transcription factor binding sites. In Third IEEE Symposium on Bioinformatics and Bioengineering, IEEE Press, Los Alamitos, pp. 214-220.
9. Blanchette,M. and Sinha,S. (2001) Separating real motifs from their artifacts. Bioinformatics, 17, S30-S38.