Abstract
We present anO(R logP) time,O(M+P 2) space algorithm for searching a restriction map withM sites for the best matches to a shorter map withP sites, whereR, the number of matching site pairs, is bounded byMP. As first proposed by Watermanet al. (1984,Nucl. Acids Res. 12, 237–242) the objective function used to score matches is additive in the number of unaligned sites and the discrepancies in the distances between adjacent aligned sites. Our algorithm is basically a sparse dynamic programming computation in which “candidate lists” are used to model the future contribution of all previously computed entries to those yet to be computed. A simple modification to the algorithm computes the distance between two restriction maps withM andN sites, respectively, inO(MN(logM+logN)) time.
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This author’s work was supported in part by National Library of Medicine Grant R01-LM4960.
This author’s work was supported in part by National Library of Medicine Grant R01-LM5110.
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Myers, E.W., Huang, X. AnO(N 2 logN) restriction map comparison and search algorithm. Bltn Mathcal Biology 54, 599–618 (1992). https://doi.org/10.1007/BF02459636
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DOI: https://doi.org/10.1007/BF02459636