Abstract
Transcription factors control transcription by binding to specific sites in the DNA sequences of the target genes, which can be modeled by structured motifs. In this paper, we propose e-BiMotif, a combination of both sequence alignment and a biclustering approach relying on efficient string matching techniques based on suffix trees to unravel all approximately conserved blocks (structured motifs) while straightforwardly disregarding non-conserved regions in-between. Since the length of conserved regions is usually easier to estimate than that of non-conserved regions separating the binding sites, ignoring the width of non-conserved regions is an advantage of the proposed method over other motif finders.
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Gonçalves, J.P., Madeira, S.C. (2010). e-BiMotif: Combining Sequence Alignment and Biclustering to Unravel Structured Motifs. In: Rocha, M.P., Riverola, F.F., Shatkay, H., Corchado, J.M. (eds) Advances in Bioinformatics. Advances in Intelligent and Soft Computing, vol 74. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13214-8_24
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DOI: https://doi.org/10.1007/978-3-642-13214-8_24
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-13213-1
Online ISBN: 978-3-642-13214-8
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