Transcription factor binding sitesBioinformatics toolsPerformance evaluationThe precise prediction of transcription factor binding sites (TFBSs) is pivotal for unraveling the gene regulatory networks underlying biological processes. While numerous tools have emerged for in silico TFBS prediction in recent years...
Prediction of transcription factor binding sites is generally performed by scanning a DNA sequence of interest with a position weight matrix (PWM) for a transcription factor of interest [6,7] and various pattern-matching tools have been developed for this purpose. These tools fall into two classes...
Although there are known transcription factor binding sites pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a DNA-MATRIX tool for searching putative transcription factor binding sites in genomic sequences. DNA-MATRIX uses...
Overall, this study provides a new and useful framework for the prediction of transcription factor binding sites by combining the funnel attention modules with the residual network. 展开 关键词: transcription factor binding site multi-scale bottom-up and top-down attention deep learning residual ...
Estimation of bound/unbound transcription factor binding sites Visualization of footprints within and across different conditions For information on each tool, please see thewiki. TOBIAS is written as a python package and can be quickly installed via pip: ...
BMO transcription factor binding prediction BMO (“Bee” MOdel of TF binding) builds on previous reports that the degree of chromatin accessibility around a motif15,16,17 and the presence of co-occurring motifs18 positively correlate with TF occupancy, corresponding to the analogy of TFs behaving ...
transcription factor binding siteFourier transformstructural fingerprintFourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In...
Cooperative binding of transcription factor (TF) dimers to DNA is increasingly recognized as a major contributor to binding specificity. However, it is likely that the set of known TF dimers is highly incomplete, given that they were discovered using ad
TFs have commonly been predicted by analyzing sequence homology with the DNA-binding domains of TFs already characterized. Thus, TFs that do not show homologies with the reported ones are difficult to predict. Here we report the development of a deep learning-based tool, DeepTFactor, that ...
observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints...