Parallel processing of biological sequence comparison algorithms
International Journal of Parallel Programming
The String-to-String Correction Problem
Journal of the ACM (JACM)
The Complexity of Some Problems on Subsequences and Supersequences
Journal of the ACM (JACM)
A linear space algorithm for computing maximal common subsequences
Communications of the ACM
A Survey of Longest Common Subsequence Algorithms
SPIRE '00 Proceedings of the Seventh International Symposium on String Processing Information Retrieval (SPIRE'00)
A Parallel Smith-Waterman Algorithm Based on Divide and Conquer
ICA3PP '02 Proceedings of the Fifth International Conference on Algorithms and Architectures for Parallel Processing
A UPC Runtime System Based on MPI and POSIX Threads
PDP '06 Proceedings of the 14th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing
A Fast Parallel Longest Common Subsequence Algorithm Based on Pruning Rules
IMSCCS '06 Proceedings of the First International Multi-Symposiums on Computer and Computational Sciences - Volume 1 (IMSCCS'06) - Volume 01
A PGAS-Based Algorithm for the Longest Common Subsequence Problem
Euro-Par '08 Proceedings of the 14th international Euro-Par conference on Parallel Processing
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An important problem in computational biology is finding the longest common subsequence (LCS) of two nucleotide sequences. This paper examines the correctness and performance of a recently proposed parallel LCS algorithm that uses successor tables and pruning rules to construct a list of sets from which an LCS can be easily reconstructed. Counterexamples are given for two pruning rules that were given with the original algorithm. Because of these errors, performance measurements originally reported cannot be validated. The work presented here shows that speedup can be reliably achieved by an implementation in Unified Parallel C that runs on an Infiniband cluster. This performance is partly facilitated by exploiting the software cache of the MuPC runtime system. In addition, this implementation achieved speedup without bulk memory copy operations and the associated programming complexity of message passing.