Parallel construction of large suffix trees on a PC cluster

Authors:
Chunxi Chen;Bertil Schmidt
Affiliations:
School of Computer Engineering, Nanyang Technological University, Singapore;School of Computer Engineering, Nanyang Technological University, Singapore
Venue:
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel Processing
Year:
2005

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Abstract

The suffix tree is a key data structure for biological sequence analysis. Even though efficient algorithms for suffix tree construction exist, for long DNA sequences such as whole human chromosomes, their run-time is still very high . In this paper we introduce a new parallel algorithm for suffix tree construction. This algorithm uses a new data structure call the common prefix suffix tree (CPST). Our parallel implementation on a PC cluster leads to significant run-time savings.