Abstract
We study biological recombination from language-theoretic and machine learning point of view. Two generative systems to model recombinations are introduced and polynomial-time algorithms for their language membership, parsing and equivalence problems are described. Another polynomial-time algorithm is given for finding a small model for a given set of recombinants.
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Creighton, H., McClintock, B.: A correlation of cytological and genetical crossingover in Zea mays. PNAS 17, 492–497 (1931)
Crochemore, M., Rytter, W.: Jewels of Stringology. World Scientific, Singapore (2002)
Daly, M., Rioux, J., Schaffner, et al.: High-resolution haplotype structure in the human genome. Nature Genetics 29, 229–232 (2001)
Koivisto, M., Perola, M., Varilo, et al.: An MDL method for finding haplotype blocks and for estimating the strength of haplotype block boundaries. In: Pacific Symposium on Biocomputing (PSB2003), pp. 502–513. World Scientific, Singapore (2003)
Patil, N., Berno, A., Hinds, D.A., et al.: Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719–1723 (2001)
Salomaa, A.: Jewels of Formal Language Theory. Computer Science Press (1981)
Sevon, P., Ollikainen, V., Toivonen, H.T.T.: Tree pattern mining for gene mapping. Information Sciences (to appear)
Ukkonen, E.: Finding founder sequences from a set of recombinants. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 277–286. Springer, Heidelberg (2002)
Zhang, K., Deng, M., Chen, T., et al.: A dynamic programming algorithm for haplotype block partitioning. PNAS 99, 7335–7339 (2002)
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© 2004 Springer-Verlag Berlin Heidelberg
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Koivisto, M., Rastas, P., Ukkonen, E. (2004). Recombination Systems. In: Karhumäki, J., Maurer, H., Păun, G., Rozenberg, G. (eds) Theory Is Forever. Lecture Notes in Computer Science, vol 3113. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-27812-2_15
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DOI: https://doi.org/10.1007/978-3-540-27812-2_15
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-22393-1
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