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We present an O (R log P) time, O (M+P2) space algorithm for searching a restriction map with M sites for the best matches to a shorter map with P sites, where R, the number of matching site pairs, is bounded by MP. As first proposed by Waterman et al. (1984, Nucl. Acids Res. 12, 237-242) the objective function used to score matches is additive in the(More)
Efficient methods for solving linear algebraic equations are crucial to creating fast and accurate numerical simulations in many applications. In this paper, an algebraic multigrid (AMG) method, which combines the classical coarsening scheme by [19] with an energy-minimizing interpolation algorithm by [26], is employed and tested for subsurface water(More)
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