Combinatorial optimization: algorithms and complexity
Combinatorial optimization: algorithms and complexity
Reconstructing a history of recombinations from a set of sequences
Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Algorithms for Association Study Design Using a Generalized Model of Haplotype Conservation
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Genotype Sequence Segmentation: Handling Constraints and Noise
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
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
Combinatorial problems arising in SNP and haplotype analysis
DMTCS'03 Proceedings of the 4th international conference on Discrete mathematics and theoretical computer science
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
A hidden markov technique for haplotype reconstruction
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Haplotype inference via hierarchical genotype parsing
WABI'07 Proceedings of the 7th 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
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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Inspired by the current interest in the so-called haplotype blocks we consider a related, complementary problem abstracted from the following scenario. We are given the DNA or SNP sequences of a sample of individuals from a (human) population. The population is assumed to have evolved as an isolate, founded some generations ago by a relatively small number of settlers. Then the sequences in our given sample should be a result of recombinations of the corresponding sequences of the founders, possibly corrupted by (rare) point mutations. We are interested in finding plausible reconstructions of the sequences of the founders. Formulated as a combinatorial string problem, one has to find a set of founder sequences such that given sequences can be composed from fragments taken from the corresponding locations of the founder sequences. The solution can be optimized for example with respect to the number of founders or the number of crossovers. We give polynomial-time algorithms for some special cases as well as a general solution by dynamic programming.