Haplotypes and informative SNP selection algorithms: don't block out information
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Haplotype reconstruction from SNP alignment
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
High-order entropy-compressed text indexes
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
A Dataset Generator for Whole Genome Shotgun Sequencing
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
The Haplotyping problem: an overview of computational models and solutions
Journal of Computer Science and Technology
Polynomial and APX-hard cases of the individual haplotyping problem
Theoretical Computer Science - Pattern discovery in the post genome
The fragment assembly string graph
Bioinformatics
ACM Computing Surveys (CSUR)
Technical comment: A clustering algorithm based on two distance functions for MEC model
Computational Biology and Chemistry
Haplotype assembly from aligned weighted SNP fragments
Computational Biology and Chemistry
On the complexity of several haplotyping problems
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
ReFHap: a reliable and fast algorithm for single individual haplotyping
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Using genetic algorithm in reconstructing single individual haplotype with minimum error correction
Journal of Biomedical Informatics
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Single nucleotide polymorphism (SNP) is the most frequent form of DNA variation. The set of SNP's present in a chromosome (called the em haplotype) is of interest in a wide area of applications in molecular biology and biomedicine, including diagnostic and medical therapy. In this paper we propose a new heuristic method for the problem of haplotype reconstruction for (portions of) a pair of homologous human chromosomes from a single individual (SIH). The problem is well known in literature and exact algorithms have been proposed for the case when no (or few) gaps are allowed in the input fragments. These algorithms, though exact and of polynomial complexity, are slow in practice. When gaps are considered no exact method of polynomial complexity is known. The problem is also hard to approximate with guarantees. Therefore fast heuristics have been proposed. In this paper we describe SpeedHap, a new heuristic method that is able to tackle the case of many gapped fragments and retains its effectiveness even when the input fragments have high rate of reading errors (up to 20%) and low coverage (as low as 3). We test SpeedHap on real data from the HapMap Project.