Finding transcription factor binding sequences
نویسندگان
چکیده
منابع مشابه
Discovering Transcription Factor Binding Motif Sequences
Introduction In biology, sequence motifs are short sequence patterns, usually with fixed lengths, that represent many features of DNA, RNA, and protein molecules. Sequence motifs can represent transcription factor binding sites for DNA, splice junctions for RNA, and binding domains for proteins. Thus, discovering sequence motifs can lead to a better understanding of transcriptional regulation, ...
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The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multiple transcription factors simultaneously in unaligned DNA sequences that may be...
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Understanding the mechanisms that determine the regulation of gene expression is an important and challenging problem. A fundamental subproblem is to identify DNA-binding sites for unknown regulatory factors, given a collection of genes believed to be coregulated, and given the noncoding DNA sequences near those genes. We present an enumerative statistical method for identifying good candidates...
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The first step in gene expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significan...
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Chromatin immunoprecipitation followed by sequencing with next-generation technologies (ChIP-Seq) has become the de facto standard for building genome-wide maps of regions bound by a given transcription factor (TF). The regions identified, however, have to be further analyzed to determine the actual DNA-binding sites for the TF, as well as sites for other TFs belonging to the same TF complex or...
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ژورنال
عنوان ژورنال: Genome Biology
سال: 2001
ISSN: 1474-760X
DOI: 10.1186/gb-2001-2-4-reports0010