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3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion

Abstract : Abstract Motivation Recent studies suggest that the loop extrusion activity of Structural Maintenance of Chromosomes complexes is central to proper organization of genomes in vivo . Polymer physics-based modeling of chromosome structure has been instrumental to assess which structures such extrusion can create. Only few laboratories however have the technical and computational expertise to create in silico models combining dynamic features of chromatin and loop extruders. Results Here we present 3DPolyS-LE, a self-contained, easy to use modeling and simulation framework allowing non-specialists to ask how specific properties of loop extruders and boundary elements impact on 3D chromosome structure. 3DPolyS-LE also provides algorithms to compare predictions with experimental Hi-C data. Availability and implementation Software available at https://gitlab.com/togop/3DPolyS-LE ; implemented in Python and Fortran 2003 and supported on any Unix-based operating system (Linux, Mac OS). Contact peter.meister@unibe.ch and daniel.jost@ens-lyon.fr Supplementary Information Supplemental data are available at Bioinformatics online
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https://hal-cnrs.archives-ouvertes.fr/hal-03797993
Contributor : Daniel Jost Connect in order to contact the contributor
Submitted on : Wednesday, October 5, 2022 - 9:08:24 AM
Last modification on : Tuesday, October 11, 2022 - 10:56:45 AM

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Todor Gitchev, Gabriel Zala, Peter Meister, Daniel Jost. 3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion. Bioinformatics, In press. ⟨hal-03797993⟩

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