Introduction

MOTIVATION: Recent experimental advancements allow determining positions of nucleosomes for complete genomes. However, the resulting nucleosome occupancy maps are averages of heterogeneous cell populations. Accordingly, they represent a snapshot of a dynamic ensemble at a single time point with an overlay of many configurations from different cells. To study the organization of nucleosomes along the genome and to understand the mechanisms of nucleosome translocation, it is necessary to retrieve features of specific conformations from the population average. RESULTS: Here, we present a method for identifying non-overlapping nucleosome configurations that combines binary-variable analysis and a Monte Carlo approach with a simulated annealing scheme. In this manner, we obtain specific nucleosome configurations and optimized solutions for the complex positioning patterns from experimental data. We apply the method to compare nucleosome positioning at transcription factor binding sites in different mouse cell types. Our method can model nucleosome translocations at regulatory genomic elements and generate configurations for simulations of the spatial folding of the nucleosome chain. AVAILABILITY: Source code, precompiled binaries, test data and a web-based test installation are freely available at http://bioinformatics.fh-stralsund.de/nucpos/

Publications

  1. Modeling nucleosome position distributions from experimental nucleosome positioning maps.
    Cite this
    Schöpflin R, Teif VB, Teif VB, Müller O, Weinberg C, Rippe K, Wedemann G, 2013-10-01 - Bioinformatics (Oxford, England)

Credits

  1. Robert Schöpflin
    Developer

    Institute for Applied Computer Science, University of Applied Sciences Stralsund, Germany

  2. Vladimir B Teif
    Developer

  3. Vladimir B Teif
    Developer

  4. Oliver Müller
    Developer

  5. Christin Weinberg
    Developer

  6. Karsten Rippe
    Developer

  7. Gero Wedemann
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006915
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByGero Wedemann