STOC '98 Proceedings of the thirtieth annual ACM symposium on Theory of computing
Reconstructing a history of recombinations from a set of sequences
Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
A linear space algorithm for computing maximal common subsequences
Communications of the ACM
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Methods for Inferring Block-Wise Ancestral History from Haploid Sequences
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Finding Founder Sequences from a Set of Recombinants
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
A hidden markov technique for haplotype reconstruction
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Minimum recombination histories by branch and bound
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Improved algorithms for inferring the minimum mosaic of a set of recombinants
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Tabu Search for the Founder Sequence Reconstruction Problem: A Preliminary Study
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
Bounds on the minimum mosaic of population sequences under recombination
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
A randomized iterated greedy algorithm for the founder sequence reconstruction problem
LION'10 Proceedings of the 4th international conference on Learning and intelligent optimization
Large neighbourhood search algorithms for the founder sequence reconstruction problem
Computers and Operations Research
Indexing a dictionary for subset matching queries
Algorithms and Applications
Minimum mosaic inference of a set of recombinants
CATS '11 Proceedings of the Seventeenth Computing: The Australasian Theory Symposium - Volume 119
Minimum mosaic inference of a set of recombinants
CATS 2011 Proceedings of the Seventeenth Computing on The Australasian Theory Symposium - Volume 119
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The within-species genetic variation due to recombinations leads to a mosaic-like structure of DNA. This structure can be modeled, e.g. by parsing sample sequences of current DNA with respect to a small number of founders. The founders represent the ancestral sequence material from which the sample was created in a sequence of recombination steps. This scenario has recently been successfully applied on developing probabilistic Hidden Markov Methods for haplotyping genotypic data. In this paper we introduce a combinatorial method for haplotyping that is based on a similar parsing idea. We formulate a polynomial-time parsing algorithm that finds minimum cross-over parse in a simplified 'flat' parsing model that ignores the historical hierarchy of recombinations. The problem of constructing optimal founders that would give minimum possible parse for given genotypic sequences is shown NP-hard. A heuristic locally-optimal algorithm is given for founder construction. Combined with flat parsing this already gives quite good haplotyping results. Improved haplotyping is obtained by using a hierarchical parsing that properly models the natural recombination process. For finding short hierarchical parses a greedy polynomial-time algorithm is given. Empirical haplotyping results on HapMap data are reported.