Abstract
Inspired by the current interest in the so-called haplotype blocks we consider a related, complementary problem abstracted from the following scenario. We are given the DNA or SNP sequences of a sample of individuals from a (human) population. The population is assumed to have evolved as an isolate, founded some generations ago by a relatively small number of settlers. Then the sequences in our given sample should be a result of recombinations of the corresponding sequences of the founders, possibly corrupted by (rare) point mutations. We are interested in finding plausible reconstructions of the sequences of the founders. Formulated as a combinatorial string problem, one has to find a set of founder sequences such that given sequences can be composed from fragments taken from the corresponding locations of the founder sequences. The solution can be optimized for example with respect to the number of founders or the number of crossovers. We give polynomial- time algorithms for some special cases as well as a general solution by dynamic programming.
Supported by the Academy of Finland under grant 22584.
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
M. Daly, J. Rioux, S. Schaffner, T. Hudson, and E. Lander. High-resolution haplotype structure in the human genome. Nature Genetics 29: 229–232, 2001.
S. B. Gabriel, S. F. Schaffner, H. Ngyen, J. M. Moore et al. The structure of haplotype blocks in the human genome. Science 296: 2225–2229, 2002.
D. Gusfield. Haplotyping as perfect phylogeny: Conceptual framework and efficient solutions. RECOMB 2002, 166–175.
R. R. Hudson and N. L. Kaplan. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147–164, 1985.
J. Kececioglu and D. Gusfield. Reconstructing a history of recombinations from a set of sequences. Discrete Applied Mathematics 88: 239–260, 1998.
H. Mannila, M. Koivisto, M. Perola, L. Peltonen, E. Ukkonen et al. A method to find and compare the strength of haplotype block boundaries. In preparation.
M. S. McPeek and A. Strahs. Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fixed-scale genetic mapping. Am.J. Hum. Genet. 65: 858–875, 1999.
C. H. Papadimitriou and K. Steiglitz. Combinatorial Optimization: Algorithms and Complexity. Dover Publications 1998.
N. Patil, A. J. Berno, D. A. Hinds, W. A. Barrett et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294: 1719–1723, 2001.
K. Zhang, M. Deng, T. Chen, M. S. Waterman and F. Sun. A dynamic programming algorithm for haplotype block partition. PNAS 99: 7335–7339, 2002.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Ukkonen, E. (2002). Finding Founder Sequences from a Set of Recombinants. In: Guigó, R., Gusfield, D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45784-4_21
Download citation
DOI: https://doi.org/10.1007/3-540-45784-4_21
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-44211-0
Online ISBN: 978-3-540-45784-8
eBook Packages: Springer Book Archive