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3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion.
Bioinformatics, 38(24):5454-5456.
SUMMARY: Recent studies suggest that the loop extrusion activity of StructuralMaintenance of Chromosomes complexes is central to proper organization of genomesin vivo. Polymer physics-based modeling of chromosome structure has beeninstrumental to assess which structures such extrusion can create. Only fewlaboratories however have the technical and computational expertise to create insilico models combining dynamic features of chromatin and loop extruders. Here,we present 3DPolyS-LE, a self-contained, easy to use modeling and simulationframework allowing non-specialists to ask how specific properties of loopextruders and boundary elements impact on 3D chromosome structure. 3DPolyS-LEalso provides algorithms to compare predictions with experimental Hi-C data.AVAILABILITY AND IMPLEMENTATION: Software available athttps://gitlab.com/togop/3DPolyS-LE; implemented in Python and Fortran 2003 andsupported on any Unix-based operating system (Linux and Mac OS). SUPPLEMENTARYINFORMATION: Supplementary information are available at Bioinformatics online.
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