Computational Biology and Chemistry
FAW '08 Proceedings of the 2nd annual international workshop on Frontiers in Algorithmics
Haplotype Assembly from Weighted SNP Fragments and Related Genotype Information
FAW '08 Proceedings of the 2nd annual international workshop on Frontiers in Algorithmics
A Practical Exact Algorithm for the Individual Haplotyping Problem MEC/GI
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A parthenogenetic algorithm for single individual SNP haplotyping
Engineering Applications of Artificial Intelligence
Model, properties and imputation method of missing SNP genotype data utilizing mutual information
Journal of Computational and Applied Mathematics
Self-organizing map approaches for the haplotype assembly problem
Mathematics and Computers in Simulation
On the Approximability of Some Haplotyping Problems
AAIM '09 Proceedings of the 5th International Conference on Algorithmic Aspects in Information and Management
A practical parameterized algorithm for the individual haplotyping problem MLF
TAMC'08 Proceedings of the 5th international conference on Theory and applications of models of computation
A combination of PSO and K-means methods to solve haplotype reconstruction problem
IIT'09 Proceedings of the 6th international conference on Innovations in information technology
A practical parameterised algorithm for the individual haplotyping problem mlf†
Mathematical Structures in Computer Science
Using genetic algorithm in reconstructing single individual haplotype with minimum error correction
Journal of Biomedical Informatics
Semi-supervised clustering algorithm for haplotype assembly problem based on MEC model
International Journal of Data Mining and Bioinformatics
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
Hi-index | 3.84 |
Motivation: Haplotype reconstruction based on aligned single nucleotide polymorphism (SNP) fragments is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. An important computational model of this problem is the minimum error correction (MEC) model, which has been mentioned in several literatures. The model retrieves a pair of haplotypes by correcting minimum number of SNPs in given genome fragments coming from an individual's DNA. Results: In the first part of this paper, an exact algorithm for the MEC model is presented. Owing to the NP-hardness of the MEC model, we also design a genetic algorithm (GA). The designed GA is intended to solve large size problems and has very good performance. The strength and weakness of the MEC model are shown using experimental results on real data and simulation data. In the second part of this paper, to improve the MEC model for haplotype reconstruction, a new computational model is proposed, which simultaneously employs genotype information of an individual in the process of SNP correction, and is called MEC with genotype information (shortly, MEC/GI). Computational results on extensive datasets show that the new model has much higher accuracy in haplotype reconstruction than the pure MEC model. Contact: wangrsh@amss.ac.cn