Second, the phrase may mean a collection of DNA sequences that conform to a common pattern (motif) and are specifically recognized by a common transcription factor. As individual binding sites for a given transcription factor are often very different, a motif is usually represented by a ...
LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser作者:Lee Chih*; Huang Chun Hsi来源:Bioinformatics, 2014, 30(13): 1923-1925.DOI:10.1093/bioinformatics/btu115摘要 LASAGNA-Search 2.0 is an integrated webtool for transcription factor (TF) binding ...
Summary: LASAGNA-Search 2.0 is an integrated webtool for transcription factor (TF) binding site search and visualization. The tool is based on the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm. It eliminates manual TF model collection and promoter sequence retrieval...
To do this, it is necessary to build a prediction model that precisely predicts the binding relationships between TFs and DNA sequences. Recently, deep learning based models have been proposed and have shown competitive results on a transcription factor binding site prediction task. However, it is...
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...
(2014). Transcription Factor Binding Site Mapping Using ChIP-Seq. Microbiology Spectrum, 2(2), 161-181. http://doi.org/10.1128/microbiolspec.MGM2-0035-2013Jaini S, Lyubetskaya A, Gomes A et al (2014) Transcription factor binding site mapping using ChIP-SEq. Microbiol Spectr 2:1-21...
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 relative to the TSS. Furthermore, near the TSS,...
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes BMC Bioinformatics, 6 (1) (2005), pp. 1-20 Google Scholar [29] Y. Wei, et al. iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multipl...
If you enter atranscription factor(e.g. SP1) you will receive the GeneIDs of the corresponding genes and the matrix families that represent the DNA binding site of this transcription factor. If you enter the name of amatrix / matrix family(e.g. V$SP1F) you will receive the GeneIDs of...
A sequence motif is a short recurring pattern with biological significance such as a DNA-recognition sequence for a transcription factor (TF), an mRNA splicing signal, or a functional region of a protein domain. Many high-throughput experimental approaches and computational tools have been developed...