Nucleosome positioning plays a major role in transcriptional regulation and most DNA-related processes. The Nucleosome Dynamics server offers different tools to analyze nucleosome positioning from MNase-seq experimental data and to compare experiments to account for the transient and dynamic nature of nucleosomes under different cellular states.
nucleR is a R/Bioconductor package for working with tiling arrays and next generation sequencing. It uses a novel aproach in this field which comprises a deep profile cleaning using Fourier Transform and peak scoring for a quick and flexible nucleosome calling.
More information is available in the associated article[1] and library can be downloaded from Bioconductor.
PCAsuite allows the user to compress Molecular Dynamics (MD) trajectories using Principal Component Analysis (PCA) algorithms. This technique offers a good compression ratio at the expense of losing some precision in the trajectory.
Single nucleotide polymorphism is the main mechanism of genetic variability in humans and the source of a large number of pathologies. PMUT predictor based on neural networks and sequence/structural information is able to predict Mendelian’s mutations with a success rate above 90%.
Protein Data Bank. Mirror to the central repository for experimental 3D structures.
pyPcazip is a suite of software tools for compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines.