Comparing Best-First Search and Dynamic Programming for Optimal Multiple Sequence Alignment

Sequence alignment is an important problem in computational biology. We compare two different approaches to the problem of optimally aligning two or more character strings: bounded dynamic programming (BDP), and divide-and-conquer frontier search (DCFS). The approaches are compared in terms of time and space requirements in 2 through 5 dimensions with sequences of varying similarity and length. While BDP performs better in two and three dimensions, it consumes more time and memory than DCFS for higher-dimensional problems.

[1]  Durbin,et al.  Biological Sequence Analysis , 1998 .

[2]  Richard E. Korf,et al.  Depth-First Iterative-Deepening: An Optimal Admissible Tree Search , 1985, Artif. Intell..

[3]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[4]  Nils J. Nilsson,et al.  A Formal Basis for the Heuristic Determination of Minimum Cost Paths , 1968, IEEE Trans. Syst. Sci. Cybern..

[5]  Esko Ukkonen,et al.  Algorithms for Approximate String Matching , 1985, Inf. Control..

[6]  J. Spouge.  Speeding up dynamic programming algorithms for finding optimal lattice paths , 1989 .

[7]  Edsger W. Dijkstra,et al.  A note on two problems in connexion with graphs , 1959, Numerische Mathematik.

[8]  Olivier Poch,et al.  BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs , 1999, Bioinform..

[9]  Richard E. Korf,et al.  Divide-and-Conquer Frontier Search Applied to Optimal Sequence Alignment , 2000, AAAI/IAAI.

[10]  Michael S. Waterman,et al.  Introduction to computational biology , 1995 .

[11]  A. Apostolio,et al.  A Fast Linear Space Algorithm for Computing Longest Common Subsequences , 1985 .

[12]  Daniel S. Hirschberg,et al.  A linear space algorithm for computing maximal common subsequences , 1975, Commun. ACM.

[13]  Jonathan Schaeffer,et al.  Memory-efficient A* heuristics for multiple sequence alignment , 2002, AAAI/IAAI.

[14]  Richard E. Korf,et al.  A Divide and Conquer Bidirectional Search: First Results , 1999, IJCAI.