cWINNOWER algorithm for finding fuzzy DNA motifs

Journal of Bioinformatics and Computational Biology

Volumn 2, Issue 1, 2004, Pages 47-60

  Liang, Shoudan ^a   Samanta, M P ^a   Biegel, B A ^a  

^a NASA AMES RESEARCH CENTER   (United States)

Author keywords

DNA motif; Transcription factor binding signals; Winnower

Indexed keywords

NUCLEOTIDE;

ARTICLE; BACILLUS SUBTILIS; COMPUTER PROGRAM; DNA DETERMINATION; DNA SEQUENCE; GENE MUTATION; GENETIC ALGORITHM; MATHEMATICAL COMPUTING; NONHUMAN; PROTEIN BINDING; PROTEIN MOTIF; RANDOMIZATION; SENSITIVITY ANALYSIS; SIGNAL DETECTION; SIGNAL TRANSDUCTION;

ALGORITHMS; AMINO ACID MOTIFS; BASE SEQUENCE; BINDING SITES; DNA; FUZZY LOGIC; GENE EXPRESSION PROFILING; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; STOCHASTIC PROCESSES;

EID: 3242888795     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720004000466     Document Type: Article

References (27)

1. B. Ren, F. Robert, J. J. Wyrick, O. Aparicio, E. J. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, T. L. Volkert, C. J. Wilson, S. P. Bell and R. A. Young, "Genome-wide location and function of DNA binding proteins," Science 290, 2306-2309 (2000).
2. V. R. Iyer, C. E. Horak, C. S. Scafe, D. Botstein, M. Snyder and P. O. Brown, "Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF," Nature 409, 533-538 (2001).
3. S. Tavazoie, J. D. Hughes, M. J. Campbell, R. J. Cho and G. M. Church, "Systematic determination of genetic network architecture," Nat. Genet. 22, 281-285 (1999).
4. Z. Zhu, Y. Pilpel and G. M. Church. "Computational identification of transcription factor binding sites via a Transcription-factor-centric Clustering (TFCC) algorithm," J. Mol. Biol. 318, 71-81 (2002).
5. N. Harafuji, D. N. Keys and M. Levine, "Genome-wide identification of tissue-specific enhancers in the Ciona tadpole," Proc. Natl. Acad. Sci. USA 99, 6802-6805 (2002).
6. E. Davidson, Genomic Regulatory Systems, Development and Evolution (Academic Press 2001).
7. G. D. Stormo, "DNA binding sites: representation and discovery," Bioinformatics 1, 16-23 (2000).
8. H. Li, "Computational approaches to identifying transcription factor binding sites in yeast genome," Methods Enzymol. 350, 484-495 (2002).
9. M. S. Gelfand, "Prediction of function in DNA sequence analysis," J. Comp. Biol. 2, 87-115 (1995).
10. K. Frech, K. Quandt and T. Werner, "Software for the analysis of DNA sequence elements of transcription," Comput. Appl. Biosci. 13, 89-97 (1997).
11. A. Brazma, I. Jonassen, I. Eidhammer and D. Gilbert, "Approaches to the automatic discovery of patterns in biosequences," J. Comp. Biol. 5, 279-305 (1998).
12. J. van Helden, B. Andre and J. Collado-Vides, "Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies," J. Mol. Biol. 281, 827-842 (1998).
13. P. A. Pevzner and S.-H. Sze, "Combinatorial approaches to finding subtle signals in DNA sequences," Proc. Int. Conf. Intell. Syst. Mol. Biol. 8, 269-278 (2000).
14. S.-H. Sze, M. S. Gelfand and P. A. Pevzner "Finding weak motifs in DNA sequences," Pac. Symp. Biocomput. 235-246 (2002).
15. C. E. Lawrence, S. F. Altschul, M. S. Boguski, J. S. Liu, A. F. Neuwald and J. C. Wooton, "Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment," Science 262, 208-214 (1993).
16. J. S. Liu, A. F. Neuwald and C. E. Lawrence, "Markovian structures in biological sequence alignments," J. Am. Statist. Assoc. 94, 1-15 (1999).
17. T. L. Bailey and C. Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers," Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36 (1994).
18. G. D. Stormo and G. W. Hartzell, 3rd, "Identifying protein-binding sites from unaligned DNA fragments," Proc. Natl. Acad. Sci. USA. 86, 1183-1187 (1989).
19. G. Z. Hertz and G. D. Stormo, "Identifying DNA and protein patterns with statistically significant alignments of multiple sequences," Bioinformatics 15, 563-577 (1999).
20. J. Buhler and M. Tompa, "Finding motifs using random projections," J. Comput. Biol. 9, 225-242 (2002).
21. R. Staden, "Methods for discovering novel motifs in nucleic acid sequences," Comput. Appl. Biosci. 5, 293-298 (1989).
22. M. Tompa, "An exact method for finding short motifs in sequences, with application to the ribosome binding site problem," Proc. Int. Conf. Intell. Syst. Mol. Biol. 262-271 (1999).
23. H. J. Bussemaker, H. Li and E. D. Siggia, "Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis," Proc. Natl. Acad. Sci. USA 97, 10096-10100 (2000).
24. X. Liu, D. L. Brutlag and J. S. Liu, "BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes," Pac. Symp. Biocomput. 127-138 (2001).
25. X. S. Liu, D. L. Brutlag and J. S. Liu, "An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitatioin microarray experiments," Nat. Biotechnol. 20, 835-839 (2002).
26. A -dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA," Nucleic Acids Res. 23, 2351-2360 (1995).
27. H. Jarmer, T. S. Larsen, A. Krogh, H. H. Saxild, S. Brunak and S. Knudsen, "Sigma A recognition sites in the Bacillus subtilis genome," Microbiology 147, 2417-2424 (2001).