Abstract
We study the single individual SNP haplotype reconstruction problem. We introduce a simple heuristic and prove experimentally that is very fast and accurate. In particular, when compared with a dynamic programming of [8] it is much faster and also more accurate. We expect Fast Hare to be very useful in practical applications. We also introduce a combinatorial problem related to the SNP haplotype reconstruction problem that we call Min Element Removal. We prove its NP-hardness in the gapless case and its O(log n)-approximability in the general case.
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Bafna, V., Halldórsson, B., Schwartz, R., Clark, A., Istrail, S.: Haplotypes and Informative SNP Selection Algorithms: Don’t Block Out Information. In: Proceedings of ACM RECOMB 2003
Garg, N., Vazirani, V., Yannakakis, M.: Multiway Cuts in Directed and Node Weighted Graphs. In: Shamir, E., Abiteboul, S. (eds.) ICALP 1994. LNCS, vol. 820, pp. 487–498. Springer, Heidelberg (1994)
Kleinberg, J., Papadimitriou, C., Raghavan, P.: Segmentation Problems. In: Proceedings of the ACM STOC, pp. 473-482 (1998)
Lancia, G.: Mathematical Programming Approaches for Computational Biology Problems, In Modelli e Algoritmi per l’Ottimizzazione di Sistemi Complessi, Agnetis and Di Pillo Eds., Pitagora Editrice, pp. 265–310
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)
The SNP Consortium, http://snp.cshl.org
Myers, G.: A Dataset Generator for Whole Genome Shotgun Sequencing. In: Proc Int Conf. Intell Syst. Mol. Biol., pp. 202-210 (1999)
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, p. 29. Springer, Heidelberg (2002)
Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources. SNPs: VARIATIONS ON A THEME, available at, http://www.ncbi.nlm.nih.gov/About/primer/snps.html
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Panconesi, A., Sozio, M. (2004). Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction. In: Jonassen, I., Kim, J. (eds) Algorithms in Bioinformatics. WABI 2004. Lecture Notes in Computer Science(), vol 3240. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30219-3_23
Download citation
DOI: https://doi.org/10.1007/978-3-540-30219-3_23
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-23018-2
Online ISBN: 978-3-540-30219-3
eBook Packages: Springer Book Archive