title: Fast matching of transcription factor motifs using generalized position weight matrix models.
abstract: The problem of finding the locations in DNA sequences that match a given motif describing the binding specificities of a transcription factor (TF) has many applications in computational biology. This problem has been extensively studied when the position weight matrix (PWM) model is used to represent motifs. We investigate it under the feature motif model, a generalization of the PWM model that does not assume independence between positions in the pattern while being compatible with the original PWM. We present a new method for finding the binding sites of a transcription factor in a DNA sequence when the feature motif model is used to describe transcription factor binding specificities. The experimental results on random and real data show that the search algorithm is fast in practice.
authors.affiliation: Department of Computer Science, University of Helsinki, Helsinki, Finland. emanuele.giaquinta@cs.helsinki.fi
authors.forename: Emanuele
authors.initials: E
authors.lastname: Giaquinta
authors.forename: Szymon
authors.initials: S
authors.lastname: Grabowski
authors.forename: Esko
authors.initials: E
authors.lastname: Ukkonen
mesh_terms: D020816:Amino Acid Motifs; D019295:Computational Biology / Q000379:methods; D008957:Models, Genetic; D020218:Response Elements / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors
references.citation: Nucleic Acids Res. 1982 May 11;10(9):2997-3011
references.pmid: 7048259
references.citation: J Mol Biol. 1986 Apr 5;188(3):415-31
references.pmid: 3525846
references.citation: Cell. 2006 Jan 13;124(1):47-59
references.pmid: 16413481
references.citation: Bioinformatics. 2009 Dec 1;25(23):3181-2
references.pmid: 19773334
references.citation: PLoS One. 2010 Mar 22;5(3):e9722
references.pmid: 20339533
references.citation: J Comput Biol. 2005 Jul-Aug;12(6):894-906
references.pmid: 16108724
references.citation: Bioinformatics. 2004 Apr 12;20(6):909-16
references.pmid: 14751969
references.citation: PLoS One. 2011;6(9):e24210
references.pmid: 21912677
references.citation: PLoS Comput Biol. 2008 Aug 22;4(8):e1000154
references.pmid: 18725950
references.citation: Proc Natl Acad Sci U S A. 1987 Jul;84(13):4355-8
references.pmid: 3474607
references.citation: J Mol Biol. 1997 Apr 25;268(1):78-94
references.pmid: 9149143
references.citation: IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):69-79
references.pmid: 21071798