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Nucleosome positioning software tools | ChIP sequencing data analysis

Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome regulation.

Source text:
(Quintales et al., 2015) Comparative analysis of methods for genome-wide nucleosome cartography. Brief Bioinform.</p

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DANPOS / Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing
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Enables comparative analysis of nucleosome physical organization at single-nucleotide resolution. DANPOS is a bioinformatics pipeline allowing dynamic analysis of nucleosome position and occupancy. The software is useful for detecting functionally relevant dynamic nucleosomes, not only in promoters in yeast, but also in distal regulatory regions with more fuzzy nucleosomes, in complex genomes such as those of mammalian.
F-Seq
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Creates a continuous tag sequence density estimation to identify biologically meaningful sites. F-Seq can summarize and display individual sequence data as an accurate and interpretable signal, allowing tag sequencing to identify specific sequence features like regions of open chromatin (DNase-seq) or transcription factor binding sites (ChIP-seq). Outputs results can be visualized through the UCSC Genome Browser.
ArchAlign
A chromatin architecture alignment algorithm. ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or tiled microarray approaches for user defined regions of interest. ArchAlign has two methods for aligning regions and three similarity/distance metrics for scoring the similarity between two regions. Depending on the data type, the user can select between Pearson or Spearman correlation, or Euclidean distance.
NPS / Nucleosome Positioning from Sequencing
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Identifies positioned nucleosome from ChIP-Seq data or nucleosome sequencing at the nucleosome level. NPS proceeds by combining the sequenced tags from all histone methylation ChIP-Seq data and using signal processing techniques. This software allows the assignation of histone methylation marks to each positioned nucleosome by exposing the key roles of nucleosome positioning and modifications in epigenetic gene regulation.
Ceres
Allows integrated analysis of nucleosome positioning and transcription factor (TF) binding sites in the promoter regions of yeast genes. Ceres is a web-based software platform that provides analysis, visualization and mining tools. The software offers five features: (1) visualization, (2) chromatin viewer, (3) gene set analysis, (4) data mining, and (5) analysis suite. It also provides access to predicted, conserved and experimentally identified binding sites throughout the yeast genome for 105 distinct yeast TFs.
NucPosSimulator
Finds positions of nucleosomes from next generation sequencing (NGS) data. NucPosSimulator combines a binary-variable analysis and a Monte Carlo simulation approach to analyze ambiguous nucleosome position data from MNase-seq experiments. The software offers a comprehensive view on possible nucleosome positions in cell ensembles and accounts for the incompatibility of mutually overlapping nucleosome configurations. It can be applied to experimental nucleosome occupancy datasets to extract important information for the functional analysis of nucleosome positions and their translocation.
ArchTEx / Architectural Tag Extender
The extension of mapped sequence tags is a common step in the analysis of single-end next-generation sequencing (NGS) data from protein localization and chromatin studies. The optimal extension can vary depending on experimental and technical conditions. Improper extension of sequence tags can obscure or mislead the interpretation of NGS results. ArchTEx identifies the optimal extension of sequence tags based on the maximum correlation between forward and reverse tags and extracts and visualizes sites of interest using the predicted extension.
NucTools
Allows calculations of nucleosome occupancy profiles averaged over several replicates, comparisons of nucleosome occupancy landscapes between different experimental conditions, and the estimation of the changes of integral chromatin properties such as the nucleosome repeat length. NucTools facilitates the annotation of nucleosome occupancy with other chromatin features like binding of transcription factors (TF) or architectural proteins, and epigenetic marks like histone modifications or DNA methylation.
PuFFIN / Positioning for Fuzzy and FIxed Nucleosomes
Builds genome-wide nucleosome maps specifically designed to take advantage of paired-end reads. PuFFIN is a method to produce a higher number of detected nucleosomes. In contrast to other approaches that require users to optimize several parameters according to their data (e.g., the maximum allowed nucleosome overlap or legal ranges for the fragment sizes), this method can accurately determine a genome-wide set of non-overlapping nucleosomes without any user-defined parameter.
NucDe
Assists in mapping nucleosome-linker boundaries from both MNase-Chip and MNase-Seq data. NucDe is an R package that uses a non-homogeneous hidden-state model based on first order differences of experimental data along genomic coordinates. It provides two functions for users: (i) nucde, for mapping nucleosome-linker boundaries from both MNase-Chip and MNase-Seq data using a non-homogeneous hidden-state model based on first order differences, and (ii) nucde.plot that plots the original signals with the nucleosome status.
nucChIP
Uses the power of ChIP-seq protocols based on enzymatic digestion. nucChIP is a set of Python and R scripts designed to be easy to use by both computational and experimental biologists. Regular ChIP-seq protocols use sonication to digest the DNA in fragment, but this method is not suitable to trace histone marks of individual nucleosomes. This limitation can be overcome by replacing sonication for enzymatic digestion to produce histone footprints with lengths similar to the amount of bases needed to wrap single nucleosomes.
Nu-OSCAR / Nucleosome-Occupancy Study for Cis-elments Accurate Recognition
Assists in identifying binding sites of known transcription factors. Nu-OSCAR is a program that incorporates nucleosome occupancy information to identify transcription factor binding sites (TFBSs) in promoter regions. This method is based on a biophysical view of equilibrium interactions between transcription factor binding and nucleosome occupancy. The code can be used to elucidate the regulatory process of gene expression.
DiNuP / differential nucleosome positioning
Obsolete
Allows comparison of nucleosome profiles generated by high-throughput sequencing under various conditions. DiNuP takes advantage of the single-nucleotide resolution of nucleosome profiles, and directly compares the distributions of sequenced nucleosome-DNA centers, along the genome, between different samples, to detect genomic regions with differential nucleosome positioning. The software also calculates P-values and empirically estimates the false discovery rate (FDR), to evaluate the statistical significance of the identified difference. It provides various parameters to characterize the physical properties of those identified regions.
START / Sequence Tag Analysis and Reporting Tool
Obsolete
Allows comprehensive analysis of serial analysis of chromatin occupancy technique (SACO) data. START is applicable to experiments performed in the yeast, fruit fly, mouse, rat and human genomes. It permits investigating the genome-wide mapping of a transcription factor (TF) of interest in an unbiased, yet cost-effective and sensitive manner. This tool integrates a wide range of genomic annotations and resources and TF binding site prediction data for a large number of genomes.
Dimnp
Obsolete
Identifies differential nucleosome regions (DNRs) in multiple samples. Dimnp is able to identify all the DNRs that are identified by two-sample method Danpos. It shows a good capacity (area under the curve > 0.87) compared with the manually identified DNRs. It can be applied in studying nucleosome variation in gradual change in development and cancer. The tool can be used in analysis of nucleosome occupancy variation and shows that promoters and telomeres enrich more of the DNRs.
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