Unification of independent collection of transcription factor binding sites and motifs. YeasTracthttp://www.yeastract.com/ Yeast-specific database. Factors, binding sites and motifs + tools. FlyReghttp://www.flyreg.org/ Drosophila DNase I Footprint Dat...
First, when the context only involves a single gene, the phrase means a short DNA sequence (typically 4鈥 30 base pairs long), which is typically located within a short distance upstream of the associated gene, and is specifically recognized by a transcription factor to control the expression ...
Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation Said et al. used cryoEM, biochemistry and bioinformatics to uncover how the Sm-like protein Rof regulates transcription termination. Rof binds termination factor ρ, inhibiting ρ rin...
In our previous studies, we found that differences in MOCCC2scores betweenk-mers associated with known canonical motifs and their variants with 1–2 base substitutions were useful for predicting changes in experimentally measured binding affinities [26,30]. Based on these observations, we investigated...
Transcription factors (TFs) form complexes that bind regulatory modules (RMs) within DNA, to control specific sets of genes. Some transcription factor binding sites (TFBSs) near the transcription start site (TSS) display tight positional preferences rela
Recently, deep learning based models have been proposed and have shown competitive results on a transcription factor binding site prediction task. However, it is difficult to interpret the prediction results obtained from the previous models. In addition, the previous models assumed all the sequence ...
Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of predicting the location of known TFBS motifs in a given DN...
Binding of transcription factors to transcription factor binding sites (TFBSs) is key to the mediation of transcriptional regulation. Information on experimentally validated functional TFBSs is limited and consequently there is a need for accurate predic
Scientists routinely scan DNA sequences for transcription factor (TF) bindingsites (TFBSs). Most of the available tools rely on position-specific scoringmatrices (PSSMs) constructed from aligned binding ...
(d) Heatmap showing the distance of de novo motifs detected per iteration (columns) to the most similar database motif (row) for significant motifs from a simulated de novo run. To the left, the number of sites from the corresponding ChIP-seq run per factor is shown as a bar plot. ...