An alignment-free model for comparison of regulatory sequences

Bioinformatics

Volumn 26, Issue 19, 2010, Pages 2391-2397

  Koohy, Hashem ^a   Dyer, Nigel P ^a   Reid, John E ^b   Koentges, Georgy ^c   Ott, Sascha ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c Department of Biological Sciences ^*  (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALGORITHM; ARTICLE; BINDING SITE; CHEMISTRY; DNA SEQUENCE; GENETIC DATABASE; GENETICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; REGULATORY SEQUENCE; SEQUENCE ALIGNMENT;

ALGORITHMS; BASE SEQUENCE; BINDING SITES; DATABASES, GENETIC; DNA; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 77957239735     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq453     Document Type: Article

References (24)

1. Aerts, S. et al. (2003) Computational detection of cis-regulatory modules. Bioinformatics, 19 (Suppl. 2), ii5-ii14.
2. Altschul, S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
3. Blaisdell, B.E. (1986) A measure of the similarity of sets of sequences not requiring sequence alignment. Proc. Natl Acad. Sci. USA, 83, 5155-5159.
4. Djordjevic, M. et al. (2003) A biophysical approach to transcription factor binding site discovery. Genome Res., 13, 2381-2390.
5. Foat, B.C. et al. (2006) Statistical mechanical modeling of genome-wide transcription factor occupancy data by matrixreduce. Bioinformatics, 22, e141-e149.
6. Gertz, J. et al. (2009) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature, 457, 215-218.
7. Hare, E.E. et al. (2008) Sepsid even-skipped enhancers are functionally conserved in drosophila despite lack of sequence conservation. PLoS Genet., 4, e1000106.
8. Kantorovitz, M.R. et al. (2007) A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics, 23, i249-i255.
9. Leung, G. and Eisen, M.B. (2009) Identifying cis-regulatory sequences by word profile similarity. PLoS One, 4, e6901.
10. Lippert, R.A. et al. (2002) Distributional regimes for the number of k-word matches between two random sequences. Proc. Natl Acad. Sci. USA, 99, 13980-13989.
11. Loo, P.V. and Marynen, P. (2009) Computational methods for the detection of cisregulatory modules. Brief. Bioinform., 10, 509-524.
12. Ludwig, M.Z. et al. (2005) Functional evolution of a cis-regulatory module. PLoS Biol., 3, e93.
13. Matys, V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
14. Needleman, S.B. andWunsch, C.D. (1970)Ageneral method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
15. Ochoa-Espinosa, A. et al. (2005) The role of binding site cluster strength in Bicoiddependent patterning in drosophila. Proc. Natl Acad. Sci. USA, 102, 4960-4965.
16. Roider, H.G. et al. (2007) Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics, 23, 134-141.
17. Segal, E. and Widom, J. (2009) From DNA sequence to transcriptional behaviour: a quantitative approach. Nat. Rev. Genet., 10, 443-456.
18. Segal, E. et al. (2008) Predicting expression patterns from regulatory sequence in drosophila segmentation. Nature, 451, 535-540.
19. Simpson-Brose, M. et al. (1994) Synergy between the hunchback and bicoid morphogens is required for anterior patterning in drosophila. Cell, 78, 855-865.
20. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
21. Tanay, A. (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res., 16, 962-972.
22. van Helden, J. (2004) Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics, 20, 399-406.
23. Vinga, S. and Almeida, J. (2003) Alignment-free sequence comparison-a review. Bioinformatics, 19, 513-523.
24. Zinzen, R.P. et al. (2009) Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature, 462, 65-70.