title: Islands of tractability for parsimony haplotyping.
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.
authors.affiliation: School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel. roded@tau.ac.il
authors.forename: Roded
authors.initials: R
authors.lastname: Sharan
authors.forename: Bjarni V
authors.initials: BV
authors.lastname: Halldósson
authors.forename: Sorin
authors.initials: S
authors.lastname: Istrail
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D044404:Genomic Islands / Q000235:genetics*; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*