Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Haplotype reconstruction from SNP alignment
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Algorithmic Graph Theory and Perfect Graphs (Annals of Discrete Mathematics, Vol 57)
Algorithmic Graph Theory and Perfect Graphs (Annals of Discrete Mathematics, Vol 57)
Parameterized Complexity
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A parthenogenetic algorithm for single individual SNP haplotyping
Engineering Applications of Artificial Intelligence
On the Approximability of Some Haplotyping Problems
AAIM '09 Proceedings of the 5th International Conference on Algorithmic Aspects in Information and Management
On the complexity of several haplotyping problems
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Using genetic algorithm in reconstructing single individual haplotype with minimum error correction
Journal of Biomedical Informatics
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
A heuristic algorithm for haplotype reconstruction from aligned weighted SNP fragments
International Journal of Bioinformatics Research and Applications
Parameterised algorithms of the individual haplotyping problem with gaps
International Journal of Bioinformatics Research and Applications
Hi-index | 0.00 |
SNP haplotyping problems have been the subject of extensive research in the last few years, and are one of the hottest areas of Computational Biology today. In this paper we report on our work of the last two years, whose preliminary results were presented at the European Symposium on Algorithms (Proceedings of the Annual European Symposium on Algorithms (ESA), Vol. 2161. Lecture Notes in Computer Science, Springer, 2001, pp. 182-193.) and Workshop on Algorithms in Bioinformatics (Proceedings of the Annual Workshop on Algorithms in Bioinformatics (WABI), Vol. 2452. Lecture Notes in Computer Science, Springer, 2002, pp. 29-43.). We address the problem of reconstructing two haplotypes for an individual from fragment assembly data. This problem will be called the Single individual Haplotyping Problem. On the positive side, we prove that the problem can be solved effectively for gapless data, and give practical, dynamic programming algorithms for its solution. On the negative side, we show that it is unlikely that polynomial algorithms exist, even to approximate the solution arbitrarily well, when the data contain gaps. We remark that both the gapless and gapped data arise in different real-life applications.