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Article Dans Une Revue Genes Année : 2022

Investigating the Diversity of Tuberculosis Spoligotypes with Dimensionality Reduction and Graph Theory

Résumé

The spoligotype is a graphical description of the CRISPR locuspresent in Mycobacterium tuberculosis, which has the particularityof having only 68 possible spacers. This spoligotype, which can beeasily obtained either in vitro or in silico, allows to have asummary information of lineage or even antibiotic resistance (whenknown to be associated to a particular cluster) at a lower cost.The objective of this article is to show that this representationis richer than it seems, and that it is under-exploited until now.We first recall an original way to represent these spoligotypes aspoints in the plane, allowing to highlight possible sub-lineages,particularities in the animal strains, etc. This graphicalrepresentation shows clusters and a skeleton in the form of agraph, which led us to see these spoligotypes as vertices of anunconnected directed graph. In this paper, we therefore propose toexploit in detail the description of the variety of spoligotypesusing a graph, and we show to what extent such a description can beinformative.

Dates et versions

hal-03932845 , version 1 (10-01-2023)

Identifiants

Citer

Gaëtan Senelle, Christophe Guyeux, Guislaine Refrégier, Christophe Sola. Investigating the Diversity of Tuberculosis Spoligotypes with Dimensionality Reduction and Graph Theory. Genes, 2022, 13 (12), pp.2328 (9). ⟨10.3390/genes13122328⟩. ⟨hal-03932845⟩
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