Showing papers by "David Eppstein published in 1989"

Efficient algorithms for sequence analysis with concave and convex gap costs

Abstract: We describe algorithms for two problems in sequence analysis: sequence alignment with gaps (multiple consecutive insertions and deletions treated as a unit) and RNA secondary structure with single loops only. We make the assumption that the gap cost or loop cost is a convex or concave function of the length of the gap or loop, and show how this assumption may be used to develop efficient algorithms for these problems. We show how the restriction to convex or concave functions may be relaxed, and give algorithms for solving the problems when the cost functions are neither convex nor concave, but can be split into a small number of convex or concave functions. Finally we point out some sparsity in the structure of our sequence analysis problems, and describe how we may take advantage of that sparsity to further speed up our algorithms.

Parallel Algorithmic Techniques for Combinatorial Computation

Abstract: We have described a number of algorithmic tools that have been found useful in the construction of parallel algorithms; among these are prefix computation, ranking, Euler tours, ear decomposition, and matrix calculations. We have also described some of the applications of these tools, and listed many other applications. These algorithms seem likely to be useful not only in their own right, but also as examples of ways to break up other problems into parts suitable for parallel solution.