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Nucleosome positioning tools

The DNA in eukaryotic cells is packed into the chromatin that is composed of nucleosomes. Positioning of the nucleosome core particles on the sequence is a problem of great interest because of the role nucleosomes play in different cellular…
NuCMap
Desktop

NuCMap

Maps directly nucleosome centers. NuCMap is based on chemical modification of…

Maps directly nucleosome centers. NuCMap is based on chemical modification of engineered histones. It locates nucleosome positions genome-wide on a map in unprecedented detail and accuracy and shows…

iNuc-STNC
Desktop

iNuc-STNC

Allows users to identify nucleosome positioning in genomes. iNuc-STNC utilizes…

Allows users to identify nucleosome positioning in genomes. iNuc-STNC utilizes various extraction techniques to find and extract salient and nominal features from nucleosome positioning sequences.…

NuPoP
Desktop

NuPoP

Predicts nucleosome position by explicitly modeling the linker DNA length.…

Predicts nucleosome position by explicitly modeling the linker DNA length. NuPoP is based on a duration Hidden Markov model (HMM). It predicts nucleosome occupancy and the most probable nucleosomes…

Epidaurus
Desktop
Web

Epidaurus

Integrative analyses of epigenetic data promise a deeper understanding of the…

Integrative analyses of epigenetic data promise a deeper understanding of the epigenome. Epidaurus is a bioinformatics tool used to effectively reveal inter-dataset relevance and differences through…

iNuc-PhysChem
Web

iNuc-PhysChem

Identifies nucleosomal sequences by incorporating physicochemical properties…

Identifies nucleosomal sequences by incorporating physicochemical properties into a 1788-Dimensional feature vector. iNuc-PhysChem was able to identify nucleosome positioning for an independent DNA…

MLM
Desktop

MLM Multi-Layer Model

Analyses nucleosome position data obtained with microarray-based approach. MLM…

Analyses nucleosome position data obtained with microarray-based approach. MLM is a classifier to distinguish between several kinds of patterns. It appears to be an important tool for the genome wide…

plot2DO
Desktop

plot2DO Plot 2D Occupancies

Allows users to plot the 2D occupancy (2DO) of genomic data. plot2DO allows the…

Allows users to plot the 2D occupancy (2DO) of genomic data. plot2DO allows the investigation of paired-end sequencing data originating from a variety of organisms. It assists user in creation of 2D…

NucEnerGen
Desktop

NucEnerGen

Predicts nucleosome energetics by using high throughput sequencing. NucEnerGen…

Predicts nucleosome energetics by using high throughput sequencing. NucEnerGen makes a prediction of nucleosome occupancy on any DNA sequence. It establishes that nucleosome occupancies can be…

nuMap
Web

nuMap

Implements the YR and W/S schemes to predict nucleosome positioning at high…

Implements the YR and W/S schemes to predict nucleosome positioning at high resolution. This methodology is based on the sequence-dependent anisotropic bending, which dictates how DNA is wrapped…

NPRD
Dataset

NPRD Nucleosome Positioning Region Database

Compiles the available experimental data on locations and characteristics of…

Compiles the available experimental data on locations and characteristics of nucleosome formation sites (NFSs). The object of the database is a single NFS described in an individual entry.

AWNFR
Desktop

AWNFR

An algorithm based on down-sampling operation and footprint in wavelet. AWNFR…

An algorithm based on down-sampling operation and footprint in wavelet. AWNFR identified regulatory regions more effectively and accurately than the previous approaches with the epigenome data in…

ICM
Web

ICM Interactive Chromatin Modeling

Allows users to assess nucleosome stability and fold sequences of DNA into…

Allows users to assess nucleosome stability and fold sequences of DNA into putative chromatin templates. ICM generates a nucleosome energy level diagram, coarse-grained representations of free DNA…

SymCurv
Desktop

SymCurv

Predicts nucleosome positions. SymCurv parses the sequence space into…

Predicts nucleosome positions. SymCurv parses the sequence space into 146-nucleotide long, non-overlapping segments in a strictly hierarchical manner. It first calculates the curvature values and…

FineStr
Web

FineStr

Allows users to upload genomic sequences in FASTA format and to perform a…

Allows users to upload genomic sequences in FASTA format and to perform a single-base-resolution nucleosome mapping on them. The site contains a help file with explanation regarding the exact usage.

nucChIP
Desktop

nucChIP

Uses the power of ChIP-seq protocols based on enzymatic digestion. nucChIP is a…

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…

Virus-ECC-mPLoc
Web

Virus-ECC-mPLoc

Predicts subcellular localization of virus proteins. Virus-ECC-mPLoc is based…

Predicts subcellular localization of virus proteins. Virus-ECC-mPLoc is based on a multi-label learning approach that can uses single-plex and multi-plex proteins to exploit correlations between…

iNuc-PseKNC
Web

iNuc-PseKNC

A predictor for predicting nucleosome positioning in Homo sapiens,…

A predictor for predicting nucleosome positioning in Homo sapiens, Caenorhabditis elegans and Drosophila melanogaster genomes.

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