Tag: Nucleosome Position

NucHunter – Inferring Nucleosome Positions from ChIP-seq Experiments

NucHunter

:: DESCRIPTION

NucHunter is an algorithm that uses the data from ChIP-seq experiments directed against many histone modifications to infer positioned nucleosomes.

::DEVELOPER

NucHunter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

 NucHunter

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 15;29(20):2547-54. doi: 10.1093/bioinformatics/btt449. Epub 2013 Aug 26.
Inferring nucleosome positions with their histone mark annotation from ChIP data.
Mammana A1, Vingron M, Chung HR.

N-score – Predict Nucleosome Positions from DNA Sequence information

N-score

:: DESCRIPTION

N-score is a wavelet analysis based model for predicting nucleosome positions from DNA sequence information.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python/Matlab

:: DOWNLOAD

 N-score

:: MORE INFORMATION

Citation

Genomic sequence is highly predictive of local nucleosome depletion.
Yuan GC, Liu JS.
PLoS Comput Biol. 2008 Jan;4(1):e13

DANPOS 2.2.2 – Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing

DANPOS 2.2.2

:: DESCRIPTION

DANPOS is designed for genome-wide comparative analysis of nucleosome maps. It detect single-nucleotide-resolution change in positions(location), enrichment (occupancy), and fuzziness (phasing, positioning) of each nucleosome unit.

::DEVELOPER

Wei Li’s Computational Epigenomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DANPOS

:: MORE INFORMATION

Citation:

Genome Res. 2013 Feb;23(2):341-51. doi: 10.1101/gr.142067.112. Epub 2012 Nov 28.
DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.
Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W.