Sequence Comparison with Mixed Convex and Concave Costs

Abstract Recently a number of algorithms have been developed for solving the minimum-weight edit sequence problem with non-linear costs for multiple insertions and deletions. We extend these algorithms to cost functions that are neither convex nor concave, but a mixture of both. We also apply this technique to related dynamic programming algorithms.

[1]  Donald E. Knuth,et al.  Breaking paragraphs into lines , 1981, Softw. Pract. Exp..

[2]  Temple F. Smith,et al.  New Stratigraphic Correlation Techniques , 1980, The Journal of Geology.

[3]  Temple F. Smith,et al.  Rapid dynamic programming algorithms for RNA secondary structure , 1986 .

[4]  Lawrence L. Larmore,et al.  The least weight subsequence problem , 1987, 26th Annual Symposium on Foundations of Computer Science (sfcs 1985).

[5]  Michael S. Waterman,et al.  General methods of sequence comparison , 1984 .

[6]  Robert E. Wilber.  The Concave Least-Weight Subsequence Problem Revisited , 1988, J. Algorithms.

[7]  Daniel J. Kleitman,et al.  An Almost Linear Time Algorithm for Generalized Matrix Searching , 1990, SIAM J. Discret. Math..

[8]  Raffaele Giancarlo,et al.  Speeding up Dynamic Programming with Applications to Molecular Biology , 1989, Theor. Comput. Sci..

[9]  E. Myers,et al.  Sequence comparison with concave weighting functions. , 1988, Bulletin of mathematical biology.

[10]  Alfred V. Aho,et al.  The Design and Analysis of Computer Algorithms , 1974 .

[11]  Alok Aggarwal,et al.  Geometric applications of a matrix-searching algorithm , 1987, SCG '86.

[12]  David Eppstein,et al.  Speeding up dynamic programming , 1988, [Proceedings 1988] 29th Annual Symposium on Foundations of Computer Science.