### Abstract

Original language | English |
---|---|

Title of host publication | Computing and Combinatorics. COCOON 2018 |

Editors | L. Wang, D. Zhu |

Publisher | Springer Verlag |

Pages | 554-566 |

DOIs | |

Publication status | Published - 29 Jun 2018 |

### Publication series

Series | Lecture Notes in Computer Science |
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Volume | 10976 |

### Cite this

*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

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*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.

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

TY - GEN

T1 - On a Fixed Haplotype Variant of the Minimum Error Correction Problem

AU - Goblet, Axel

AU - Kelk, Steven

AU - Mihalák, Matúš

AU - Stamoulis, Georgios

PY - 2018/6/29

Y1 - 2018/6/29

N2 - 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.

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.

U2 - 10.1007/978-3-319-94776-1_46

DO - 10.1007/978-3-319-94776-1_46

M3 - Conference article in proceeding

T3 - Lecture Notes in Computer Science

SP - 554

EP - 566

BT - Computing and Combinatorics. COCOON 2018

A2 - Wang, L.

A2 - Zhu, D.

PB - Springer Verlag

ER -