Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes

Nucleic Acids Research

Volumn 38, Issue 2, 2009, Pages

  Li, Guojun ^a,b   Liu, Bingqiang ^a,b,c   Xu, Ying ^a,c  

^a UNIVERSITY OF GEORGIA   (United States)

^b SHANDONG UNIVERSITY   (China)

^c BioEnergy Science Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

REGULATOR PROTEIN;

ACCURACY; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE SEQUENCE; GENOME ANALYSIS; MOLECULAR RECOGNITION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROKARYOTE; PROMOTER REGION; PROTEIN MOTIF; RELIABILITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SIMULATION; BACTERIAL GENOME; COMPUTER SIMULATION; DNA SEQUENCE; ESCHERICHIA COLI K 12; EVALUATION; GENETICS; GENOMICS; METHODOLOGY; MUTATION;

PROKARYOTA;

COMPUTER SIMULATION; ESCHERICHIA COLI K12; GENOME, BACTERIAL; GENOMICS; MUTATION; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 77951167204     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp907     Document Type: Article

References (23)

1. Stormo, G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
2. GuhaThakurta, D. (2006) Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res., 34, 3585-3598.
3. Tompa, M., Li, N., Bailey, T.L., Church, G.M., De Moor, B., Eskin, E., Favorov, A.V., Frith, M.C., Fu, Y., Kent, W.J. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144.
4. Neuwald, A.F., Liu, J.S. and Lawrence, C.E. (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci., 4, 1618-1632.
5. Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouze, P. and Moreau, Y. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J. Comput. Biol., 9, 447-464.
6. Chen, X., Guo, L., Fan, Z. and Jiang, T. (2008) W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data. Bioinformatics, 24, 1121-1128.
7. Baily, T.L. and Elkan, C.P. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Mach. Learn., 21, 51-80.
8. Pevzner, P.A. and Sze, S.H. (2000) Combinatorial approaches to finding subtle signals in DNA sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8, 269-278.
9. Zhang, S., Xu, M., Li, S. and Su, Z. (2009) Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Res., 37, e72.
10. Stormo, G.D. and Hartzell, G.W. III. (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA, 86, 1183-1187.
11. Hertz, G.Z. and Stormo, G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
12. Lawrence, C.E. and Reilly, A.A. (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins, 7, 41-51.
13. 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.
14. Liu, Z., Guo, J.T., Li, T. and Xu, Y. (2008) Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach. Proteins, 72, 1114-1124.
15. Zhang, J., Jiang, B., Li, M., Tromp, J., Zhang, X. and Zhang, M.Q. (2007) Computing exact P-values for DNA motifs. Bioinformatics, 23, 531-537.
16. Staden, R. (1989) Methods for calculating the probabilities of finding patterns in sequences. Comput. Appl. Biosci., 5, 89-96.
17. Bailey, T.L. and Gribskov, M. (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics, 14, 48-54.
18. da Fonseca, P.G., Guimaraes, K.S. and Sagot, M.F. (2008) Efficient representation and P-value computation for high-order Markov motifs. Bioinformatics, 24, i160-i166.
19. Bembom, O., Keles, S. and van der Laan, M.J. (2007) Supervised detection of conserved motifs in DNA sequences with cosmo. Stat. Appl. Genet. Mol. Biol., 6, Article8.
20. Gama-Castro, S., Jimenez-Jacinto, V., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M.I., Contreras-Moreira, B., Segura-Salazar, J., Muniz-Rascado, L., Martinez-Flores, I., Salgado, H. et al. (2008) RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res., 36, D120-D124.
21. 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.
22. Keseler, I.M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I.T., Peralta-Gil, M. and Karp, P.D. (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res., 33, D334-D337.
23. Nagarajan, N., Jones, N. and Keich, U. (2005) Computing the P-value of the information content from an alignment of multiple sequences. Bioinformatics, 21(Suppl. 1), i311-i318.