Comparative analysis of methods for representing and searching for transcription factor binding sites
نویسندگان
چکیده
منابع مشابه
Comparative analysis of methods for representing and searching for transcription factor binding sites
MOTIVATION An important step in unravelling the transcriptional regulatory network of an organism is to identify, for each transcription factor, all of its DNA binding sites. Several approaches are commonly used in searching for a transcription factor's binding sites, including consensus sequences and position-specific scoring matrices. In addition, methods that compute the average number of nu...
متن کاملAnalysis of Pairwise Dependency Information Content for Representing and Searching for Transcription Factor Binding Sites
Transcription factors are proteins that are able to bind to certain segments of DNA to control gene expression. We present an improvement upon supervised learning approaches used for finding transcription factor binding sites. We look at binding sites of the same length for a single transcription factor and use the Berg and von Hippel scoring method. Pairwise information content of positional d...
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In the post-genomic era, identification of specific regulatory motifs or transcription factor binding sites (TFBSs) in non-coding DNA sequences, which is essential to elucidate transcriptional regulatory networks, has emerged as an obstacle that frustrates many researchers. Consequently, numerous motif discovery tools and correlated databases have been applied to solving this problem. However, ...
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...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2004
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bth438