AliBiMotif: Integrating alignment and biclustering to unravel transcription factor binding sites in DNA sequences

Authors:
Joana P. Gonçalves;Yves Moreau;Sara C. Madeira
Affiliations:
Knowledge Discovery and Bioinformatics (KDBIO), INESC-ID Computer Science Department, IST, Technical University of Lisbon, Rua Alves Redol 9, 1000-029 Lisboa, Portugal;BIOI, Electrical Engineering Dept. (ESAT-SCD), KULeuven, Kasteelpark Arenberg 10, 3001 Heverlee, Belgium;Knowledge Discovery and Bioinformatics (KDBIO), INESC-ID Computer Science Department, IST, Technical University of Lisbon, Rua Alves Redol 9, 1000-029 Lisboa, Portugal
Venue:
International Journal of Data Mining and Bioinformatics
Year:
2012

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Abstract

Transcription Factors (TFs) control transcription by binding to specific sites in the promoter regions of the target genes, which can be modelled by structured motifs. In this paper we propose AliBiMotif, a method combining sequence alignment and a biclustering approach based on efficient string matching techniques using suffix trees to unravel approximately conserved sets of blocks (structured motifs) while straightforwardly disregarding non-conserved stretches in-between. The ability to ignore the width of non-conserved regions is a major advantage of the proposed method over other motif finders, as the lengths of the binding sites are usually easier to estimate than the separating distances.