Islands of tractability for parsimony haplotyping

Roded Sharan, Bjarni V. Halldórsson, Sorin Istrail

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

Abstract

We study the parsimony approach to haplotype inference, which calls for finding a set of haplotypes of minimum cardinality that explains an input set of genotypes. We prove that the problem is APX-hard even in very restricted cases. On the positive side, we identify islands of tractability for the problem, by focusing on instances with specific structure of haplotype sharing among the input genotypes. We exploit the structure of those instance to give polynomial and constant-approximation algorithms to the problem. We also show that the general parsimony haplotyping problem is fixed parameter tractable.

Original languageEnglish
Title of host publicationProceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005
Pages65-72
Number of pages8
DOIs
StatePublished - 2005
Event2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005 - Stanford, CA, United States
Duration: 8 Aug 200511 Aug 2005

Publication series

NameProceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005
Volume2005

Conference

Conference2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005
Country/TerritoryUnited States
CityStanford, CA
Period8/08/0511/08/05

Keywords

  • Approximation algorithm
  • Complexity
  • Fixed parameter tractability
  • Genotype
  • Haplotype inference
  • Parsimony

Fingerprint

Dive into the research topics of 'Islands of tractability for parsimony haplotyping'. Together they form a unique fingerprint.

Cite this