Conference Paper

Parallel chaining algorithms

Abouelhoda M.
Mohamed H.

Given a set of weighted hyper-rectangles in a k-dimensional space, the chaining problem is to identify a set of colinear and non-overlapping 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. © 2010 Springer-Verlag.