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)

NUCwave v1 – Generates Nucleosome Occupation Maps

NUCwave v1

:: DESCRIPTION

NUCwave is a bioinformatic tool that generates nucleosome occupation maps.

::DEVELOPER

Francisco Antequera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • Python

:: DOWNLOAD

 NUCwave

:: MORE INFORMATION

Citation

Brief Bioinform. 2014 Oct 8. pii: bbu037
Comparative analysis of methods for genome-wide nucleosome cartography.
Quintales L, Vázquez E, Antequera F.

NucleoFinder 1.0 – Detection of Nucleosome Positions

NucleoFinder 1.0

:: DESCRIPTION

NucleoFinder addresses both the positional heterogeneity across cells and experimental biases by seeking nucleosomes consistently positioned in a cell population and showing a significant enrichment relative to a control sample.

:: DEVELOPER

Chris Holmes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package

:: DOWNLOAD

 NucleoFinder

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Mar 15;29(6):711-716. Epub 2013 Jan 6.
NucleoFinder: a statistical approach for the detection of nucleosome positions.
Becker J, Yau C, Hancock JM, Holmes CC.