NPS 1.3.2 – Nucleosome Positioning from Sequencing

NPS 1.3.2

:: DESCRIPTION

NPS (Nucleosome Positioning from Sequencing) is a signal processing-based algorithm for identifying positioned nucleosomes fromsequencing experiments at the nucleosome level.The software is a python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level. NPS obtains continuous wave-form that represents the enrichment of histone modifications (or nucleosomes) by extending each tag (25nt, Solexa) to 150nt in the 3’ direction and taking the middle 75, and detects the positions of nucleosomes based on Laplacian of Gaussian (LOG) edge detection. The p value of each detection was estimated using Poisson approximation and the user can decide a cut-off for the final selection of nucleosome positions. In case of histone modification, the sequence tags are regrouped by different types of histone modification after nucleosome positioning and then the p-value of a particular histone modification at a positioned nucleosome was calculated based on the tag count of that histone modification in the nucleosome region using Poisson distribution, similar to the method mentioned above. The user also can select a cut-off of p value in histone modification assignment.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NPS

:: MORE INFORMATION

Citation:

Zhang Y, Shin H, Song JS, Lei Y, Liu XS.
Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq.
BMC Genomics 2008, 9:537.

Nucleosee – Visual Genome-wide search of Nucleosome Patterns

Nucleosee

:: DESCRIPTION

Nucleosome is web-based nucleosome map visual browser backed up by BWT-based pattern searches. It can be used for other kinds of high-throughput genomic data as well.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

Nucleosee

:: MORE INFORMATION

Citation

Santamaría, R., Therón, R., Durán, L., García, A., González, S., Sánchez, M., & Antequera, F. (2019).
Genome-wide search of nucleosome patterns using visual analytics.
Bioinformatics, 35(13), 2185-2192

iNuc-force – Identify Nucleosome Positions in Genome

iNuc-force

:: DESCRIPTION

iNuc-force allows for discriminating nucleosome-enriched regions from nucleosome-depleted regions.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions.
Liu G, Liu GJ, Tan JX, Lin H.
Genomics. 2019 Sep;111(5):1167-1175. doi: 10.1016/j.ygeno.2018.07.013.

iNuc-PhysChem – Identification of Nucleosomes in S.cerevisiae Genome

iNuc-PhysChem

:: DESCRIPTION

iNuc-PhysChem is a sequence-based predictor for identifying nucleosomes via physicochemical properties

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(10):e47843. doi: 10.1371/journal.pone.0047843. Epub 2012 Oct 29.
iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.
Chen W1, Lin H, Feng PM, Ding C, Zuo YC, Chou KC.

iNuc-PseKNC – Predicting Nucleosomes with Pseudo K-tuple Nucleotide Composition

iNuc-PseKNC

:: DESCRIPTION

The web-server iNuc-PseKNC was developed to predict nucleosome occupancy of H. sapiens, C. elegan and D. melanogaster

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition.
Guo SH, Deng EZ, Xu LQ, Ding H, Lin H, Chen W, Chou KC.
Bioinformatics. 2014 Jun 1;30(11):1522-9. doi: 10.1093/bioinformatics/btu083.

nuMap – Accurate Prediction of Nucleosome Positioning

nuMap

:: DESCRIPTION

nuMap implements the YR and W/S schemes to predict nucleosome positioning at high resolution.

::DEVELOPER

nuMap team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

nuMap: a web platform for accurate prediction of nucleosome positioning.
Alharbi BA, Alshammari TH, Felton NL, Zhurkin VB, Cui F.
Genomics Proteomics Bioinformatics. 2014 Oct;12(5):249-53. doi: 10.1016/j.gpb.

FineStr 1.0 – Single-base-resolution Nucleosome Positioning

FineStr 1.0

:: DESCRIPTION

FineStr (pronounced as (fi-nes’tru), from Latin fenestra—window, and from fine structure]) server allows users to upload genomic sequences in FASTA format and to perform a single-base-resolution nucleosome mapping on them.

::DEVELOPER

FineStr team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Mar 15;26(6):845-6. doi: 10.1093/bioinformatics/btq030. Epub 2010 Jan 26.
FineStr: a web server for single-base-resolution nucleosome positioning.
Gabdank I1, Barash D, Trifonov EN.

PuFFIN – Build Nucleosome Maps from paired-end Reads

PuFFIN

:: DESCRIPTION

PuFFIN (Positioning for Fuzzy and FIxed Nucleosomes) is a command line tool for accurate placing of the nucleosomes based on the pair-end reads. It was designed to place non-overlapping nucleosomes using extra lenght information present in pair-end data-sets.

::DEVELOPER

PuFFIN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 PuFFIN

:: MORE INFORMATION

Citation

PuFFIN–a parameter-free method to build nucleosome maps from paired-end reads.
Polishko A, Bunnik EM, Le Roch KG, Lonardi S.
BMC Bioinformatics. 2014;15 Suppl 9:S11. doi: 10.1186/1471-2105-15-S9-S11.

NOrMAL – Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model

NOrMAL beta2

:: DESCRIPTION

NOrMAL (NucleOsome Mapping ALgorithm) is a command line tool for accurate placing of the nucleosomes. It was designed to resolve overlapping nucleosomes and extract extra information (“fuzziness”, probability, etc.) of nucleosome placement.

::DEVELOPER

NOrMAL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 NOrMAL

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 15;28(12):i242-9. doi: 10.1093/bioinformatics/bts206.
NORMAL: accurate nucleosome positioning using a modified Gaussian mixture model.
Polishko A1, Ponts N, Le Roch KG, Lonardi S.

NSeq – Java software for Nucleosome Positioning

NSeq

:: DESCRIPTION

NSeq is a multithreaded Java application for finding positioned nucleosomes from sequencing data

::DEVELOPER

Jun S. Song’s Research Group

:: SCREENSHOTS

nseq

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • Java

:: DOWNLOAD

 NSeq

:: MORE INFORMATION

Citation

A. Nellore, K. Bobkov, E. Howe, A. Pankov, A. Diaz, J.S. Song.
NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data,
Frontiers in Genetics, 3:320 (2013)