Variable structure motifs for transcription factor binding sites
نویسندگان
چکیده
منابع مشابه
From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites
Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) became a method of choice to locate DNA segments bound by different regulatory proteins. ChIP-Seq produces extremely valuable information to study transcriptional regulation. The wet-lab workflow is often supported by downstream computational analysis including construction of models of nucleotide sequences of transcription fa...
متن کاملBayesian Clustering of Transcription Factor Binding Motifs
Genes are often regulated in living cells by proteins called transcription factors (TFs) that bind directly to short segments of DNA in close proximity to specific genes. These binding sites have a conserved nucleotide appearance, which is called a motif. Several recent studies of transcriptional regulation require the reduction of a large collection of motifs into clusters based on the similar...
متن کاملPseudocounts for transcription factor binding sites
To represent the sequence specificity of transcription factors, the position weight matrix (PWM) is widely used. In most cases, each element is defined as a log likelihood ratio of a base appearing at a certain position, which is estimated from a finite number of known binding sites. To avoid bias due to this small sample size, a certain numeric value, called a pseudocount, is usually allocated...
متن کاملStructure-Based Ab Initio Prediction of Transcription Factor–Binding Sites
We present an all-atom molecular modeling method that can predict the binding specificity of a transcription factor based on its 3D structure, with no further information required. We use molecular dynamics and free energy calculations to compute the relative binding free energies for a transcription factor with multiple possible DNA sequences. These sequences are then used to construct a posit...
متن کاملA Bayesian Clustering Model for Transcription Factor Binding Motifs
Genes are often regulated in living cells by proteins called transcription factors that bind directly to short segments of DNA in close proximity to certain target genes. These short segments have a conserved appearance, which is called a motif. We propose a Bayesian hierarchical clustering model for the common structure between a set of discovered motifs. This clustering model utilizes a Diric...
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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2010
ISSN: 1471-2164
DOI: 10.1186/1471-2164-11-30