On a Fixed Haplotype Variant of the Minimum Error Correction Problem

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademicpeer-review

Abstract

Haplotype assembly is the problem of reconstructing the two parental chromosomes of an individual from a set of sampled dna-sequences. A combinatorial optimization problem that models haplotype assembly is the minimum error correction problem (mec). This problem has been intensively studied in the computational biology literature and is also known in the clustering literature: essentially we are required to find two cluster centres such that the sum of distances to the nearest centre, is minimized. We introduce here the problem fixed haplotype-minimum error correction (fh-mec), a new variant of mec which corresponds to instances where one of the haplotypes/centres is already given. We provide hardness results for the problem on various restricted instances. We also propose a new and very simple 2-approximation algorithm for mec on binary input matrices.
Original languageEnglish
Title of host publicationComputing and Combinatorics. COCOON 2018
EditorsL. Wang, D. Zhu
PublisherSpringer Verlag
Pages554-566
DOIs
Publication statusPublished - 29 Jun 2018

Publication series

SeriesLecture Notes in Computer Science
Volume10976

Cite this

Goblet, A., Kelk, S., Mihalák, M., & Stamoulis, G. (2018). On a Fixed Haplotype Variant of the Minimum Error Correction Problem. In L. Wang, & D. Zhu (Eds.), Computing and Combinatorics. COCOON 2018 (pp. 554-566). Springer Verlag. Lecture Notes in Computer Science, Vol.. 10976 https://doi.org/10.1007/978-3-319-94776-1_46
Goblet, Axel ; Kelk, Steven ; Mihalák, Matúš ; Stamoulis, Georgios. / On a Fixed Haplotype Variant of the Minimum Error Correction Problem. Computing and Combinatorics. COCOON 2018. editor / L. Wang ; D. Zhu. Springer Verlag, 2018. pp. 554-566 (Lecture Notes in Computer Science, Vol. 10976).
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abstract = "Haplotype assembly is the problem of reconstructing the two parental chromosomes of an individual from a set of sampled dna-sequences. A combinatorial optimization problem that models haplotype assembly is the minimum error correction problem (mec). This problem has been intensively studied in the computational biology literature and is also known in the clustering literature: essentially we are required to find two cluster centres such that the sum of distances to the nearest centre, is minimized. We introduce here the problem fixed haplotype-minimum error correction (fh-mec), a new variant of mec which corresponds to instances where one of the haplotypes/centres is already given. We provide hardness results for the problem on various restricted instances. We also propose a new and very simple 2-approximation algorithm for mec on binary input matrices.",
author = "Axel Goblet and Steven Kelk and Mat{\'u}š Mihal{\'a}k and Georgios Stamoulis",
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Goblet, A, Kelk, S, Mihalák, M & Stamoulis, G 2018, On a Fixed Haplotype Variant of the Minimum Error Correction Problem. in L Wang & D Zhu (eds), Computing and Combinatorics. COCOON 2018. Springer Verlag, Lecture Notes in Computer Science, vol. 10976, pp. 554-566. https://doi.org/10.1007/978-3-319-94776-1_46

On a Fixed Haplotype Variant of the Minimum Error Correction Problem. / Goblet, Axel; Kelk, Steven; Mihalák, Matúš; Stamoulis, Georgios.

Computing and Combinatorics. COCOON 2018. ed. / L. Wang; D. Zhu. Springer Verlag, 2018. p. 554-566 (Lecture Notes in Computer Science, Vol. 10976).

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademicpeer-review

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AB - Haplotype assembly is the problem of reconstructing the two parental chromosomes of an individual from a set of sampled dna-sequences. A combinatorial optimization problem that models haplotype assembly is the minimum error correction problem (mec). This problem has been intensively studied in the computational biology literature and is also known in the clustering literature: essentially we are required to find two cluster centres such that the sum of distances to the nearest centre, is minimized. We introduce here the problem fixed haplotype-minimum error correction (fh-mec), a new variant of mec which corresponds to instances where one of the haplotypes/centres is already given. We provide hardness results for the problem on various restricted instances. We also propose a new and very simple 2-approximation algorithm for mec on binary input matrices.

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Goblet A, Kelk S, Mihalák M, Stamoulis G. On a Fixed Haplotype Variant of the Minimum Error Correction Problem. In Wang L, Zhu D, editors, Computing and Combinatorics. COCOON 2018. Springer Verlag. 2018. p. 554-566. (Lecture Notes in Computer Science, Vol. 10976). https://doi.org/10.1007/978-3-319-94776-1_46