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Computer vision for pattern detection in chromosome contact maps

Abstract : Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols.
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https://hal-pasteur.archives-ouvertes.fr/pasteur-03263561
Contributor : Axel Cournac <>
Submitted on : Thursday, June 17, 2021 - 1:59:21 PM
Last modification on : Tuesday, July 13, 2021 - 3:29:33 AM

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Distributed under a Creative Commons Attribution 4.0 International License

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Cyril Matthey-Doret, Lyam Baudry, Axel Breuer, Rémi Montagne, Nadège Guiglielmoni, et al.. Computer vision for pattern detection in chromosome contact maps. Nature Communications, Nature Publishing Group, 2020, 11 (1), pp.5795. ⟨10.1038/s41467-020-19562-7⟩. ⟨pasteur-03263561⟩

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