Optimal haplotype reconstruction in half-sib families

11 pages•Published: May 15, 2012

Aurélie Favier, Jean-Michel Elsen, Simon de Givry and Andrés Legarra

Abstract

In the goal of genetic improvement of livestock by marker assisted selection, we aim at reconstructing the haplotypes of sires from their offspring. We reformulate this problem into a weighted binary constraint satisfaction problem with only equality and disequality soft constraints. Our results show these problems have a small treewidth and can be solved optimally, improving haplotype reconstruction compared to previous approaches especially for small families (<10 descendants).

Keyphrases: haplotpes, treewidth, weighted constraint satisfaction problem

In: Agostino Dovier, Alessandro Dal Palù and Sebastian Will (editors). WCB10. Workshop on Constraint Based Methods for Bioinformatics, vol 4, pages 27-37.

Links:	https://easychair.org/publications/paper/SpJ
	https://doi.org/10.29007/rpn1

BibTeX entry

@inproceedings{WCB10:Optimal_haplotype_reconstruction_half,
  author    = {Aurélie Favier and Jean-Michel Elsen and Simon de Givry and Andrés Legarra},
  title     = {Optimal haplotype reconstruction in half-sib families},
  booktitle = {WCB10. Workshop on Constraint Based Methods for Bioinformatics},
  editor    = {Agostino Dovier and Alessandro Dal Palù and Sebastian Will},
  series    = {EPiC Series in Computing},
  volume    = {4},
  publisher = {EasyChair},
  bibsource = {EasyChair, https://easychair.org},
  issn      = {2398-7340},
  url       = {/publications/paper/SpJ},
  doi       = {10.29007/rpn1},
  pages     = {27-37},
  year      = {2012}}

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