Bryan M. Franklin
Steven Seidel
ABSTRACT
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.
- S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. Basic local alignment search tool. J. Mol. Biol., 215(3):403--410, October 1990.Google Scholar
Cross Ref
- M. Bakhouya, O. Serres, and T. El-Ghazawi. A pgas-based algorithm for the longest common subsequence problem. In Euro-Par '08: Proceedings of the 14th international Euro-Par conference on Parallel Processing, pages 654--664, Berlin, Heidelberg, 2008. Springer-Verlag. Google ScholarDigital Library
- L. Bergroth, H. Hakonen, and T. Raita. A survey of longest common subsequence algorithms. International Symposium on String Processing and Information Retrieval, 0:39, 2000. Google ScholarDigital Library
- Elizabeth E. Edmiston, Nolan G. Core, Joel H. Saltz, and Roger M. Smith. Parallel processing of biological sequence comparison algorithms. Int. J. Parallel Program., 17(3):259--275, 1988. Google ScholarDigital Library
- Bryan M. Franklin and Steven Seidel. Analysis and performance of a UPC implementation of a parallel longest common subsequence algorithm. Technical Report CS-TR-09-01, Michigan Technological University, December 2009.Google Scholar
- Adam R. Galper and Douglas L. Brutlag. Parallel similarity search and alignment with the dynamic programming method. Technical report, Stanford University, California, 1990.Google Scholar
- D. S. Hirschberg. A linear space algorithm for computing maximal common subsequences. Commun. ACM, 18(6):341--343, 1975. Google ScholarDigital Library
- Wei Liu, Yixin Chen, Ling Chen, and Ling Qin. A fast parallel longest common subsequence algorithm based on pruning rules. First International Multi-Symposiums on Computer and Computational Sciences, 2006. IM-SCCS06., 1:27--34, June 2006. Google ScholarDigital Library
- David Maier. The complexity of some problems on subsequences and supersequences. J. ACM, 25(2):322--336, 1978. Google ScholarDigital Library
- Saul B. Needleman and Christian D. Wunsch. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3):443--453, March 1970.Google ScholarCross Ref
- W. R. Pearson and D. J. Lipman. Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America, 85(8):2444--2448, 1988.Google ScholarCross Ref
- T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. Journal of Molecular Biology, 147(1):195--197, March 1981.Google ScholarCross Ref
- Robert A. Wagner and Michael J. Fischer. The string-to-string correction problem. J. ACM, 21(1):168--173, 1974. Google ScholarDigital Library
- Fa Zhang, Xiang-Zhen Qiao, and Zhi-Yong Liu. A parallel smith-waterman algorithm based on divide and conquer. In Fifth International Conference on Algorithms and Architectures for Parallel Processing, 2002, pages 162--169, 2002. Google ScholarDigital Library
- Z. Zhang, J. Savant, and S. Seidel. A UPC Runtime System based on MPI and POSIX Threads. In Proc. of 14th Euromicro Conference on Parallel, Distributed and Network-based Processing (PDP 2006), 2006. Google ScholarDigital Library
Recommendations
A BSP/CGM Algorithm for the All-Substrings Longest Common Subsequence Problem
IPDPS '03: Proceedings of the 17th International Symposium on Parallel and Distributed ProcessingGiven two strings X and Y of lengths mand n, respectively, the all-substrings longest common subsequence (ALCS) problem obtains the lengths of the subsequences common to X and any substring of Y . The sequential algorithm takes O(mn) time and O(n) ...
SCI Networking for Shared-Memory Computing in UPC: Blueprints of the GASNet SCI Conduit
LCN '04: Proceedings of the 29th Annual IEEE International Conference on Local Computer NetworksUnified Parallel C (UPC) is a programming model for shared-memory parallel computing on shared- and distributed-memory systems. The Berkeley UPC software, which operates on top of their Global Addressing Space Networking (GASNet) communication system, ...
A PGAS-Based Algorithm for the Longest Common Subsequence Problem
Euro-Par '08: Proceedings of the 14th international Euro-Par conference on Parallel ProcessingFinding the Longest Common Subsequence (LCS) is a traditional and well studied problem in bioinformatics and text editing. In this paper, a customized parallel algorithm based on the Partitioned Global Address Space (PGAS) programming model to compute ...
Comments