The main input parameters for the ChromHL calculations are (i) the DNA sequence, (ii) weight matrices of size 4 x m setting DNA binding affinities for each protein type g which covers m(g) bp upon binding, (iii) binding constants K(n,g) for protein binding to a nucleosome in ...
Several examples given in Figure 3 show that DNA can be, for example, bent, kinked, elongated, and wrapped around a protein. Many lines of experimental evidence suggest that the energetic cost of distorting the DNA into a particular conformation is sequence dependent, and this dependence is ...
The twenty-first century is a biology-technology developing century. We know that a gene is made of DNA. The nucleotide bases from which DNA is built are A(adenine), C(cytosine), G(guanine), and T(thymine). Finding the longest common subsequence between DNA/Protein sequences is one of ...
Unique sequences Protein encoding genes—comprising upstream regulatory region, exons, and introns Genes encoding non-translated RNA (snRNA, snoRNA, 7SL RNA, telomerase RNA, Xist RNA, a variety of small regulatory RNAs) Non-repetitive intragenic non-coding DNA ...
feature_file="example_data/CDD_protein_feature.txt") # 2 dataset = data.encode(thread=20) # 3 model = GCNmodel.model(label_num=2, other_feature_dim=206).to(device) # 4 GCNmodel.train(dataset, model, weighted_sampling=True) # 5 ...
The binding specificities of RNA- and DNA-binding proteins are determined from experimental data using a ‘deep learning’ approach. Knowing the sequence specificities of DNA- and RNA-binding proteins is essential for developing models of the regulatory
Knowledge of the sequence of a DNA segment has many uses. First, it can be used to find genes, segments of DNA that code for a specificproteinorphenotype. If a region of DNA has been sequenced, it can be screened for characteristic features of genes. For example, open reading frames (...
Nucleotide sequence coding for the fusion protein of the virus of the Newcastle disease or for an equivalent polypeptide is determined, the fusion product is expressed, for example, in E. coli or in a yeast; the sequence can be employed with the aim of vaccination or for diagnosis.DANIELE ...
telomeres consist of repeat sequences and are bound by multiple telomeric interacting proteins. In mammalian cells, telomere DNA is composed of double-stranded tandem repeats ofTTAGGG, with terminal 3′ G-rich single-stranded overhangs. Telomeres are protected by protein complexes, such as shelterin,...
Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins...