Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies
نویسندگان
چکیده
منابع مشابه
Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes
MOTIVATION We present a sequence-based framework and algorithm PHYLOCLUS for predicting co-regulated genes. In our approach, de novo discovery methods are used to find motifs conserved by evolution and then a Bayesian hierarchical clustering model is used to cluster these motifs, thereby grouping together genes that are putatively co-regulated. Our clustering procedure allows both the number of...
متن کاملAssessing phylogenetic motif models for predicting transcription factor binding sites
MOTIVATION A variety of algorithms have been developed to predict transcription factor binding sites (TFBSs) within the genome by exploiting the evolutionary information implicit in multiple alignments of the genomes of related species. One such approach uses an extension of the standard position-specific motif model that incorporates phylogenetic information via a phylogenetic tree and a model...
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The binding affinity of DNA-binding proteins such as transcription factors is mainly determined by the base composition of the corresponding binding site on the DNA strand. Most proteins do not bind only a single sequence, but rather a set of sequences, which may be modeled by a sequence motif. Algorithms for de novo motif discovery differ in their promoter models, learning approaches, and othe...
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Summary Recent studies have shown that the traditional position weight matrix model is often insufficient for modeling transcription factor binding sites, as intra-motif dependencies play a significant role for an accurate description of binding motifs. Here, we present the Java application InMoDe, a collection of tools for learning, leveraging and visualizing such dependencies of putative high...
متن کاملOn the value of intra-motif dependencies of human insulator protein CTCF
The modularity of the ZOOPS model allows for combining an arbitrary motif model with parameters Θm with an arbitrary flanking model with parameters Θf. The binary latent variable ui handles the situation that the i-th sequence contains (ui = 1) or contains not (ui = 0) a binding site. We model the position of the binding site of width W by the latent variable vi ∈ {1, . . . , Li −W + 1}. The bi...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2017
ISSN: 1471-2105
DOI: 10.1186/s12859-017-1495-1