A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length

Bioinformatics

Volumn 21, Issue 10, 2005, Pages 2240-2245

  Favorov, A V ^a   Gelfand, M S ^a,b   Gerasimova, A V ^a   Ravcheev, D A ^b,c   Mironov, A A ^a,c   Makeev, V J ^a,d  

^a STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

^b INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^c MOSCOW STATE UNIVERSITY   (Russian Federation)

^d ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

AEROBIC RESPIRATION CONTROL PROTEIN A; BACTERIAL PROTEIN; DEOXYRIBONUCLEOPROTEIN; PALINDROMIC DNA;

ALGORITHM; ARTICLE; BACTERIAL GENE; BAYES THEOREM; BINDING SITE; COMPUTER PROGRAM; DNA SEQUENCE; DNA STRUCTURE; ESCHERICHIA COLI; GENETIC ANALYSIS; GEOMETRY; MATHEMATICAL COMPUTING; MONTE CARLO METHOD; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN MOTIF; REGULON;

ARCA; ESCHERICHIA COLI;

EID: 19544379737     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti336     Document Type: Article

References (41)

1. Bailey,T. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning J., 21, 51-83.
2. Berg,O.G. and von Hippel,P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
3. Besag,J. et al. (1996) Bayesian computation and stochastic systems. Stat. Sci., 10, 3-66.
4. Bulyk,M. (2003) Computational prediction of transcription-factor binding site locations. Genome Biol., 5, 201.
5. Chiang,D.Y. et al. (2003) Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol., 4, R43.
6. Crooks,G.E. et al. (2004) Weblogo: a sequence logo generator. Genome Res., 1188-1190.
7. Darwin,A.J. and Stewart,V. (1995) Expression of the narX, narL, narP, and narQ genes of Escherichia coli K-12: regulation of the regulators. J. Bacteriol., 177, 3865-3869.
8. Darwin,A.J. et al. (1997) Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement. Mol. Microbiol., 25, 583-595.
9. Favorov,A.V. et al. (2002) Yet another digging for DNA motifs Gibbs sampler. In Proceedings of BGRS 2002, Novisibisk, 1, 31-33.
10. Frith,M.C. et al. (2003) Cluster-Buster: finding dense clusters of motifs in DNA sequences. Nucleic Acids Res., 31, 3666-3668.
11. Gelfand,M.S. et al. (2000) Comparative analysis of regulatory patterns in bacterial genomes. Brief. Bioinformatics, 1, 357-371.
12. Geman,S. and Geman,D. (1984) Stochastic relaxation, Gibbs distribution and the Bayesian restoration of images. IEEE Trans. Patt. Anal. Mac. Intell., 6, 621-641.
13. Gerasimova,A.V. et al. (2003) ArcA regulator of gamma-proteobacteria: identification of the binding signal and description of the regulon. Biophysics (Moscow), 48, 21-25.
14. Harbison,C.T. et al. (2004) Transcription regulatory code of a eukaryotic genome. Nature, 431, 99-104.
15. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
16. Hughes,J.D. et al. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
17. Kel-Margoulis,O.V. et al. (2002) TRANSCompel: a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res., 30, 332-334.
18. Lawrence,C.E. et al. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
19. Li,H. et al. (2002) Identification of the binding sites of regulatory proteins in bacterial genomes. Proc. Natl Acad. Sci. USA, 99, 11772-11777.
20. Liu,J.S. (2001) Monte Carlo Strategies in Scientific Computing. Springer-Verlag, NY, Berlin, Heidelberg.
21. Liu,X. and De Wulf,P. (2004) Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling. J. Biol. Chem., 279, 12588-12597.
22. Liu,X.S. et al. (2002) An algorithm for finding protein DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835-839.
23. Lynch,A.S. and Lin,E.C. (1996) Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters. J. Bacteriol., 178, 6238-6249.
24. Makeev,V.J. et al. (2003) Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res., 31, 6016-6026.
25. Maris,A.E. et al. (2002) Dimerization allows DNA target site recognition by the NarL response regulator. Nat. Struct. Biol., 9, 771-778.
26. McGuire,A.M. et al. (1999) A weight matrix for binding recognition by the redox-response regulator ArcA-P of Escherichia coli. Mol. Microbiol., 32, 219-221.
27. Mironov,A.A. et al. (1999) Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res., 27, 2981-2989.
28. Mironov,A.A. et al. (2000) Software for analyzing bacterial genomes. Mol. Biol. (Mosk), 34, 253-262.
29. Mwangi,M.M. and Siggia,E.D. (2003) Genome wide identification of regulatory motifs in Bacillus subtilis. BMC Bioinformatics, 4, 18.
30. Pilpel,Y. et al. (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet., 29, 153-159.
31. Qiu,P. et al. (2002) Computational analysis of composite regulatory elements. Mamm. Genome, 13, 327-332.
32. Robert,C.P. (1998) Discretization and MCMC Convergence Assessment. Springer-Verlag, NY, Berlin, Heidelberg.
33. Robin,S. et al. (2002) Occurrence probability of structured motifs in random sequences. J. Comp. Biol., 9, 761-773
34. Roth,F.P. et al. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotech., 16, 939-945.
35. Schneider,T.D. and Stephens,R.M. (1990) Sequence Logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
36. Sivia,D.S. (1996) Data Analysis. A Bayesian Tutorial. Clarendon Press, Oxford.
37. Stormo,G.D. and Hartzell,G.W. III (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA, 86, 1183-11877.
38. Thijs,G. et al. (2002) A Gibbs sampling method to detect over-represented motifs in the upstream regions of coexpressed genes. J. Comp. Biol., 9, 447-464.
39. Thompson,W. et al. (2003) Gibbs recursive sampler: finding transcription factor binding sites. Nucleic Acids Res., 31, 3580-3585.
40. Tompa,M. et al. (2005) An assessment of computational tools for the discovery of transcription factor binding sites, Nat. Biotech., 23, 137-144.
41. van Helden,J. et al. (2000) Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res., 28, 1808-1818.