Hardware Implementation of the Smith-Waterman Algorithm Using Recursive Variable Expansion

Provided by: Delft University of Technology
Topic: Hardware
Format: PDF
Sequence alignment is an important activity in the field of bioinformatics that enables the user to compare DNA strands with each other and promises to help the user understand possible genetically transmitted diseases. In this paper, the authors adapted a novel approach for accelerating the Smith-Waterman (S-W) algorithm using Recursive Variable Expansion (RVE), which exposes extra parallelism in the algorithm, as compared to any other technique. The results demonstrate that applying the recursive variable expansion technique speeds up the performance by a factor of 1.36 to 1.41, as compared to traditional acceleration approaches at the cost of using 1.25 to 1.28 times more hardware resources.

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