RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Polynomial and APX-hard cases of the individual haplotyping problem
Theoretical Computer Science - Pattern discovery in the post genome
Complexity and approximation of the minimum recombinant haplotype configuration problem
Theoretical Computer Science
Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms
INFORMS Journal on Computing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Combinatorial problems arising in SNP and haplotype analysis
DMTCS'03 Proceedings of the 4th international conference on Discrete mathematics and theoretical computer science
Complexity and approximation of the minimum recombination haplotype configuration problem
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Hi-index | 0.00 |
In this paper we describe a method for statistical reconstruction of haplotypes from a set of aligned SNP fragments. We consider the case of a pair of homologous human chromosomes, one from the mother and the other from the father. After fragment assembly and SNP detection, we wish to reconstruct the two haplotypes of the parents. Given a set of SNP sites inferred from the assembly alignment, we wish to divide the fragment set into two subsets, each of which represents one chromosome. Our method is based on a statistical model of sequencing errors, compositional information and haplotype memberships.We calculate probabilities of different haplotypes conditional on the alignment. Due to computational complexity, we first determine phases for neighboring SNPs. Then we connect them and construct haplotype segments. Also we compute the accuracy or confidence of the reconstructed haplotypes. We discuss other issues such as alternative methods, parameter estimation, computational efficiency, and relaxation of assumptions.