Parallel dynamic programming for solving the string editing problem on a CGM/BSP

Authors:
C. E. R. Alves;E. N. Cáceres;F. Dehne
Affiliations:
FTCE - Universidade São, São Paulo, Brazil;Universidade Federal de Mato, Campo Grande, Brazil;Carleton University, Ottawa, Canada
Venue:
Proceedings of the fourteenth annual ACM symposium on Parallel algorithms and architectures
Year:
2002

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Abstract

In this paper we present a coarse-grained parallel algorithm for solving the string edit distance problem for a string A and all substrings of a string C. Our method is based on a novel CGM/BSP parallel dynamic programming technique for computing all highest scoring paths in a weighted grid graph. The algorithm requires \log p rounds/supersteps and O(\fracn^2p\log m) local computation, where $p$ is the number of processors, p^2 \leq m \leq n. To our knowledge, this is the first efficient CGM/BSP algorithm for the alignment of all substrings of C with A. Furthermore, the CGM/BSP parallel dynamic programming technique presented is of interest in its own right and we expect it to lead to other parallel dynamic programming methods for the CGM/BSP.