Extended islands of tractability for parsimony haplotyping

Authors:
Rudolf Fleischer;Jiong Guo;Rolf Niedermeier;Johannes Uhlmann;Yihui Wang;Mathias Weller;Xi Wu
Affiliations:
School of Computer Science, IIPL, Fudan University, Shanghai, China;Universität des Saarlandes, Saarbrücken, Germany;Institut für Informatik, Friedrich-Schiller-Universität Jena, Jena, Germany;Institut für Informatik, Friedrich-Schiller-Universität Jena, Jena, Germany;School of Computer Science, IIPL, Fudan University, Shanghai, China;Institut für Informatik, Friedrich-Schiller-Universität Jena, Jena, Germany;School of Computer Science, IIPL, Fudan University, Shanghai, China
Venue:
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Year:
2010

Citing 9
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Abstract

Parsimony haplotyping is the problem of finding a smallest size set of haplotypes that can explain a given set of genotypes. The problem is NP-hard, and many heuristic and approximation algorithms as well as polynomial-time solvable special cases have been discovered. We propose improved fixed-parameter tractability results with respect to the parameter "size of the target haplotype set" k by presenting an O*(k4k)-time algorithm. This also applies to the practically important constrained case, where we can only use haplotypes from a given set. Furthermore, we show that the problem becomes polynomial-time solvable if the given set of genotypes is complete, i.e., contains all possible genotypes that can be explained by the set of haplotypes.