Article Dans Une Revue Theoretical Computer Science Année : 2024

Sorting genomes by prefix double-cut-and-joins

Résumé

In this paper, we study the problem of sorting unichromosomal linear genomes by prefix doublecut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and recombine the severed endpoints in one of two possible ways: one of these options corresponds to a prefix reversal, which reverses the order of elements between the two cuts (as well as their signs in the signed case). Our main results are:

(1) new structural lower bounds based on the breakpoint graph for sorting by unsigned prefix reversals, unsigned prefix DCJs, and signed prefix DCJs; (2) two polynomial-time algorithms for sorting by prefix DCJs, both in the signed case (which answers an open question of Labarre [1]) and in the unsigned case; (3) a 1-absolute approximation algorithm for sorting by unsigned prefix reversals for a specific class of permutations.

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hal-04901649 , version 1 (20-01-2025)

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Guillaume Fertin, Géraldine Jean, Anthony Labarre. Sorting genomes by prefix double-cut-and-joins. Theoretical Computer Science, 2024, 1024, pp.114909. ⟨10.1016/j.tcs.2024.114909⟩. ⟨hal-04901649⟩
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