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Parameterized Algorithms in Bioinformatics: An Overview

Centre national de la recherche scientifique (CNRS), Université Paris-Est Marne-la-Vallée, 77454 Marne-la-Vallée, France
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Algorithms 2019, 12(12), 256; https://doi.org/10.3390/a12120256
Received: 30 September 2019 / Revised: 11 November 2019 / Accepted: 19 November 2019 / Published: 1 December 2019
(This article belongs to the Special Issue New Frontiers in Parameterized Complexity and Algorithms)
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.
Keywords: fixed-parameter tractability; genome assembly; sequence analysis; comparative genomics; haplotyping; phylogenetics; agreement forests fixed-parameter tractability; genome assembly; sequence analysis; comparative genomics; haplotyping; phylogenetics; agreement forests
MDPI and ACS Style

Bulteau, L.; Weller, M. Parameterized Algorithms in Bioinformatics: An Overview. Algorithms 2019, 12, 256.

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