Methodological Developments for Studying Genetic Variability in Animal Populations

• Title: "Methodological developments for studying genetic variability in animal populations" INRAE.
  • PhD student: Siegfried Dubois.
  • Affiliated unit: INRAE, UMR 1388 - GenPhySe - Cytogene.
  • Co-supervision:
    • Thomas Faraut (INRAE);
    • Claire Lamaitre (Inria).
  • Doctoral school: Matisse - Mathématiques, télécommunications, informatique, signal, systèmes, électronique.
  • Project duration: 2023–2026.

Project summary:

Pangenome graphs are data structures that represent a multiple sequence alignment (MSA) in the form of a particular directed graph. Their construction method largely relies on heuristics: changing a parameter or using a different tool yields a different graph. In an initial attempt to better understand the variation information integrated into the graph, we developed a method based on the concept of edit distance to identify differences between pangenome graphs, which we implemented and tested on graphs built from yeast genomes.