Abstract
The algorithms that are based on the Weighted Minimum Letter Flips (WMLF) model are more accurate in haplotype reconstruction than those based on the Minimum Letter Flips (MLF) model, but WMLF is effective only when the error rate in SNP fragments is low. In this paper, we first establish a new computational model that employs the related genotype information as an improvement of the WMLF model and show its NP-hardness, and then we propose an efficient genetic algorithm to solve for the haplotype assembly problem. The results of experiments on a real data set indicate that the introduction of genotype information to the WMLF model is quite effective in improving the reconstruction rate especially when the error rate in SNP fragments is high.
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
Cilibrasi, R., Iersel, L.V., Kelk, S., Tromp, J.: On the Complexity of Several Haplotyping Problems. In: Casadio, R., Myers, G. (eds.) WABI 2005. LNCS (LNBI), vol. 3692, pp. 128–139. Springer, Heidelberg (2005)
Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J., Lander, E.S.: High-resolution haplotype structure in the human genome. Nature Genetics 29, 229–232 (2001)
Greenberg, H.J., Hart, W.E., Lancia, G.: Opportunities for Combinatorial Optimization in Computational Biology. INFORMS Journal on Computing 16(3), 211–231 (2004)
Goldberg, D.E.: Genetic Algorithms in serarch, Optimization and Machine Learning. Addison-Wesley, Reading (1989)
Rizzi, R., Bafna, V., Istrail, S., Lancia, G.: Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 29–43. Springer, Heidelberg (2002)
Stephens, J.C., et al.: Haplotype variation and linkage disequilibrium in 313 human genes. Science 293, 489–493 (2001)
Terwilliger, J.D., Weiss, K.M.: Linkage disequilibrium mapping of complex disease: fantasy or reality? Current Opinion in Biotechnology 9(6), 578–594 (1998)
Wang, Y., Feng, E., Wang, R., Zhang, D.: The haplotype assembly model with genotype information and iterative local-exhaustive search algorithm. Computational Biology and Chemistry 31, 288–293 (2007)
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, 105–114 (2006)
Zhang, X.S., Wang, R.S., Wu, L.Y., Zhang, W.: Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype. Evolutionary Bioinformatics Online 2, 271–280 (2006)
Zhao, Y.Y., Wu, L.Y., Zhang, J.H., Wang, R.S., Zhang, X.S.: Haplotype assembly from aligned weighted SNP fragments. Computational Biology and Chemistry 29, 281–287 (2005)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kang, SH., Jeong, IS., Choi, MH., Lim, HS. (2008). Haplotype Assembly from Weighted SNP Fragments and Related Genotype Information. In: Preparata, F.P., Wu, X., Yin, J. (eds) Frontiers in Algorithmics. FAW 2008. Lecture Notes in Computer Science, vol 5059. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69311-6_8
Download citation
DOI: https://doi.org/10.1007/978-3-540-69311-6_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-69310-9
Online ISBN: 978-3-540-69311-6
eBook Packages: Computer ScienceComputer Science (R0)