Similarity of position frequency matrices for transcription factor binding sites
نویسندگان
چکیده
منابع مشابه
Similarity of position frequency matrices for transcription factor binding sites
MOTIVATION Transcription-factor binding sites (TFBS) in promoter sequences of higher eukaryotes are commonly modeled using position frequency matrices (PFM). The ability to compare PFMs representing binding sites is especially important for de novo sequence motif discovery, where it is desirable to compare putative matrices to one another and to known matrices. RESULTS We describe a PFM simil...
متن کاملTranscription Factor Binding Sites: Position-Specific and Position-Dependent Modeling
Transcription of a gene is cued by the binding of a protein to a binding site. Transcription factors bind to specific binding sites (TFBSs), of which there may be many for a single transcription factor (1). However, these TFBSs often exhibit a considerable amount of variability, as the sequences consist of similar nucleotides rather than complete replicas of a TFBS (1). The ability to model the...
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BACKGROUND Identifying transcription factor binding sites (TFBS) in silico is key in understanding gene regulation. TFBS are string patterns that exhibit some variability, commonly modelled as "position weight matrices" (PWMs). Though convenient, the PWM has significant limitations, in particular the assumed independence of positions within the binding motif; and predictions based on PWMs are u...
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Accurate prediction of transcription factor binding sites (TFBSs) is a prerequisite for identifying cis-regulatory modules that underlie transcriptional regulatory circuits encoded in the genome. Here, we present a computational framework for detecting TFBSs, when multiple position weight matrices (PWMs) for a transcription factor are available. Grouping multiple PWMs of a transcription factor ...
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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/bth480