On Weight Matrix and Free Energy Models for Sequence Motif Detection
نویسندگان
چکیده
منابع مشابه
On Weight Matrix and Free Energy Models for Sequence Motif Detection
The problem of motif detection can be formulated as the construction of a discriminant function to separate sequences of a specific pattern from background. In computational biology, motif detection is used to predict DNA binding sites of a transcription factor (TF), mostly based on the weight matrix (WM) model or the Gibbs free energy (FE) model. However, despite the wide applications, theoret...
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MOTIVATION AND RESULTS The position weight matrix (PWM) is a popular method to model transcription factor binding sites. A fundamental problem in cis-regulatory analysis is to "count" the occurrences of a PWM in a DNA sequence. We propose a novel probabilistic score to solve this problem of counting PWM occurrences. The proposed score has two important properties: (1) It gives appropriate weigh...
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A three dimensional model of the basic Helix-Loop-Helix motif and its sequence specific recognition of DNA is described. The basic-helix I is modeled as a continuous ?-helix because no ?-helix breaking residue is found between the basic region and the first helix. When the basic region of the two peptide monomers are aligned in the successive major groove of the cognate DNA, the hydrophobi...
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0957-4174/$ see front matter 2011 Elsevier Ltd. A doi:10.1016/j.eswa.2011.04.133 q This document is a collaborative effort. ⇑ Corresponding authors. Tel.: +1 404 413 5703. E-mail addresses: [email protected] (W. Kim), [email protected] (J. Kim), [email protected] (Y. Pa Park). The problem of discovering motifs from protein sequences is a critical and challenging task in the field of bioinformatics...
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In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern sequence or weight matrix. Although there are known transcription factor binding sites databases available for genome wide prediction but no tool is available whic...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2010
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2009.0142