Prefix and suffix reversals on strings

Fertin, Guillaume; Jankowiak, Loïc; Jean, Géraldine

doi:10.1016/j.dam.2017.07.031

Cited by 2 publications

(1 citation statement)

References 11 publications

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“…No polynomial-time algorithm is known for computing these rearrangement distances, although NP-completeness is still open, notably on permutations for signed prefix reversals and prefix transpositions. Fixed-parameter tractability results may be achieved in the permutation model using the relationship between these rearrangements and breakpoints [24], and in the string model using the number of blocks b max as a parameter [21,25].…”

Section: Sorting By Reversals (Sbr)mentioning

confidence: 99%

Parameterized Algorithms in Bioinformatics: An Overview

Bulteau¹,

Weller²

2019

Algorithms

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Bioinformatics regularly poses new challenges to algorithm engineers and theoretical computer scientists. This work surveys recent developments of parameterized algorithms and complexity for important NP-hard problems in bioinformatics. We cover sequence assembly and analysis, genome comparison and completion, and haplotyping and phylogenetics. Aside from reporting the state of the art, we give challenges and open problems for each topic.

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Section: Sorting By Reversals (Sbr)mentioning

confidence: 99%

Parameterized Algorithms in Bioinformatics: An Overview

Bulteau¹,

Weller²

2019

Algorithms

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Rearrangement Distance Problems: An updated survey

Oliveira,

Brito,

Alexandrino

et al. 2024

ACM Comput. Surv.

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One of the challenges in the Comparative Genomics field is to infer how close two organisms are based on the similarities and differences between their genetic materials. Recent advances in DNA sequencing have made complete genomes increasingly available. That said, several new algorithms trying to infer the distance between two organisms based on genome rearrangements have been proposed in the literature. However, given the diversity of approaches, the diversity of genome rearrangement events, or even how each work models the genomes and what assumptions are made by each of them, finding the ideal algorithm for each situation or simply knowing the range of applicable approaches can be challenging. In this work, we review these approaches having the algorithmic and combinatorial advances since 2010 as our main focus. This survey aims to organize the recently published papers using a concise notation and to indicate the gaps filled by each of them in the literature. This makes it easier to understand what still needs to be done and what has room for enhancement.

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Prefix and suffix reversals on strings

Cited by 2 publications

References 11 publications

Parameterized Algorithms in Bioinformatics: An Overview

Parameterized Algorithms in Bioinformatics: An Overview

Rearrangement Distance Problems: An updated survey

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