SSP'05 -- Proceedings

	IEEE/SP 13th workshop on Statistical Signal Processing July, 17-20, 2005 - Bordeaux - France

Information regarding the paper

Title

Finding Transcription Factor Binding Sites in DNA Sequences : A Template Based Approach

Author(s)

Sumedha Gunewardena	Oxford University Computing Laboratory
Zhaolei Zhang	Charles H. Best Institute, University of Toronto

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Abstract

A problem faced by many algorithms for finding transcription factor binding sites is the high number of false positive hits that result with the increased sensitivity of their prediction. A main contributing factor to this is the short and degenerate nature of these sites which results in a low signal to noise ratio. In order to counter this problem one needs to look beyond the base independence assumption. We propose a model based on templates designed to capture not only sequence homology but also structural homology and nucleotide polymorphisms that may be present in these sites.