Parallel chaining algorithms

Authors:
Mohamed Abouelhoda;Hisham Mohamed
Affiliations:
Center for Informatics Sciences, Nile University, Giza, Egypt;Center for Informatics Sciences, Nile University, Giza, Egypt
Venue:
EuroMPI'10 Proceedings of the 17th European MPI users' group meeting conference on Recent advances in the message passing interface
Year:
2010

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Abstract

Given a set of weighted hyper-rectangles in a k-dimensional space, the chaining problem is to identify a set of colinear and nonoverlapping hyper-rectangles of total maximal weight. This problem is used in a number of applications in bioinformatics, string processing, and VLSI design. In this paper, we present parallel versions of the chaining algorithm for bioinformatics applications, running on multi-core and computer cluster architectures. Furthermore, we present experimental results of our implementations on both architectures.