Sorting by Multi-cut Rearrangements - Archive ouverte HAL
Communication Dans Un Congrès Année : 2021

Sorting by Multi-cut Rearrangements

Résumé

Let S be a string built on some alphabet Σ. A multi-cut rearrangement of S is a string S′ obtained from S by an operation called k-cut rearrangement, that consists in (1) cutting S at a given number k of places in S, making S the concatenated string X1⋅X2⋅X3…Xk⋅Xk+1, where X1 and Xk+1 are possibly empty, and (2) rearranging the Xis so as to obtain S′=Xπ(1)⋅Xπ(2)⋅Xπ(3)…Xπ(k+1), π being a permutation on 1,2…k+1 satisfying π(1)=1 and π(k+1)=k+1. Given two strings S and T built on the same multiset of characters from Σ, the Sorting by Multi-cut Rearrangements (SMCR) problem asks whether a given number ℓ of k-cut rearrangements suffices to transform S into T. The SMCR problem generalizes and thus encompasses several classical genomic rearrangements problems, such as Sorting by Transpositions and Sorting by Block Interchanges. It may also model chromoanagenesis, a recently discovered phenomenon consisting in massive simultaneous rearrangements. In this paper, we study the SMCR problem from an algorithmic complexity viewpoint, and provide, depending on the respective values of k and ℓ, polynomial-time algorithms as well as NP-hardness, FPT-algorithms, W[1]-hardness and approximation results, either in the general case or when S and T are permutations.

Dates et versions

hal-03346830 , version 1 (16-09-2021)

Identifiants

Citer

Laurent Bulteau, Guillaume Fertin, Géraldine Jean, Christian Komusiewicz. Sorting by Multi-cut Rearrangements. SOFSEM 2021, Jan 2021, Bolzano-Bozen, Italy. pp.593-607, ⟨10.1007/978-3-030-67731-2_43⟩. ⟨hal-03346830⟩
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