MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.
- Resource Type
- Academic Journal
- Authors
- Rossini R; Department of Biosciences, University of Oslo, 0316, Oslo, Norway.; Kumar V; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318, Oslo, Norway.; Mathelier A; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318, Oslo, Norway.; Rognes T; Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316, Oslo, Norway.; Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0424, Oslo, Norway.; Paulsen J; Department of Biosciences, University of Oslo, 0316, Oslo, Norway. jonas.paulsen@ibv.uio.no.; Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316, Oslo, Norway. jonas.paulsen@ibv.uio.no.
- Source
- Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE
- Subject
- Language
- English
DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.
(© 2022. The Author(s).)