Abstract
Given the genotype and the aligned single nucleotide polymorphism (SNP) fragments of an individual, Minimum Error Correction with Genotype Information (MEC/GI) is an important computational model to infer a pair of haplotypes compatible with the genotype by correcting minimum number of SNPs in the given SNP fragments. For the problem, there has been no practical exact algorithm. In DNA sequencing experiments, due to technical limits, the maximum length of a fragment sequenced directly is about 1kb. In consequence, the maximum number k of SNP sites that a fragment covers is usually small (usually smaller than 10). Based on the observation above, the current paper introduces a new parameterized dynamic programming algorithm of running time O(m k 2k + mlogm + mk), where m is the number of fragments. The algorithm solves the MEC/GI problem efficiently even if the number of fragments and SNPs are large, and is practical in real biological applications.
This research was supported in part by the National Natural Science Foundation of China under Grant Nos. 60433020 and 60773111, the National Basic Research 973 Program of China No.2008CB317107, the Program for New Century Excellent Talents in University No. NCET-05-0683, the Program for Changjiang Scholars and Innovative Research Team in University No. IRT0661, and the Scientific Research Fund of Hunan Provincial Education Department under Grant No.06C526.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Gabriel, S.B., Schaffner, S.F., Nguyen, H., et al.: The Structure of Haplotype Blocks in the Human Genome. Science 296(5576), 2225–2229 (2002)
Gusfield, D.: An Overview of Combinatorial Methods for Haplotype Inference. In: Istrail, S., Waterman, M.S., Clark, A. (eds.) DIMACS/RECOMB Satellite Workshop 2002. LNCS (LNBI), vol. 2983, pp. 9–25. Springer, Heidelberg (2004)
Hinds, D.A., Stuve, L.L., Nilsen, G.B., et al.: Whole-Genome Patterns of Common DNA Variation in Three Human Populations. Science 307(5712), 1072–1079 (2005)
Lancia, G., Bafna, V., Istrail, S., Lippert, R., Schwartz, R.: SNPs Problems, Complexity and Algorithms. In: Meyer auf der Heide, F. (ed.) ESA 2001. LNCS, vol. 2161, pp. 182–193. Springer, Heidelberg (2001)
Myers, G.: A Dataset Generator for Whole Genome Shotgun Sequencing. In: Lengauer, T., Schneider, R., Bork, P., et al. (eds.) Proc. ISMB 1999, pp. 202–210. AAAI Press, California (1999)
Panconesi, A., Sozio, M.: Fast Hare: a Fast Heuristic for Single Individual SNP Haplotype Reconstruction. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 266–277. Springer, Heidelberg (2004)
Sanger, F., Nicklen, S., Coulson, A.R.: DNA Sequencing with Chain-Terminating Inhibitors. PNAS 74(12), 5463–5467 (1977)
Stephens, J.C., Schneider, J.A., Tanguay, D.A., et al.: Haplotype Variation and Linkage Disequilibrium in 313 Human Genes. Science 293(5529), 489–493 (2001)
The International HapMap Consortium: A Haplotype Map of the Human Genome. Nature 437(7063), 1299–1320 (2005)
The International SNP Map Working Group: A Map of Human Genome Sequence Variation Containing 1.42 Million Single Nucleotide Polymorphisms. Nature 409(6822), 928–933 (2001)
Wang, D.G., Fan, J.B., Siao, C.J., et al.: Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome. Science 280(5366), 1077–1082 (1998)
Wang, R.S., Wu, L.Y., Li, Z.P., Zhang, X.S.: Haplotype Reconstruction from SNP Fragments by Minimum Error Correction. Bioinformatics 21(10), 2456–2462 (2005)
Zhang, X.S., Wang, R.S., Wu, L.Y., Chen, L.: Models and Algorithms for Haplotyping Problem. Current Bioinformatics 1(1), 105–114 (2006)
Zhang, X., Wang, R., Wu, L., Zhang, W.: Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype. Evolutionary Bioinformatics 2, 271–280 (2006)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Xie, M., Wang, J., Chen, J. (2008). A Practical Exact Algorithm for the Individual Haplotyping Problem MEC/GI. In: Hu, X., Wang, J. (eds) Computing and Combinatorics. COCOON 2008. Lecture Notes in Computer Science, vol 5092. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69733-6_34
Download citation
DOI: https://doi.org/10.1007/978-3-540-69733-6_34
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-69732-9
Online ISBN: 978-3-540-69733-6
eBook Packages: Computer ScienceComputer Science (R0)