1 - 24 of 24 results


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.


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.


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.

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.

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.


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.


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.

START / Sequence Tag Analysis and Reporting Tool

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.