Bio-Sequence Analysis with Cradle's 3SoC#8482; Software Scalable System on Chip

摘要

With the dramatically increasing amounts of genomic sequence database, there is a need for faster and more sensitive searching for sequence similarity analysis. The Smith-Waterman algorithm, which utilizes dynamic programming, is a common method for performing exact local alignments between two protein or DNA sequences. The Smith-Waterman algorithm is exhaustive and generally considered to be the most sensitive, but long computation times limit the use of this algorithm. This paper presents a preliminary implementation of Smith-Waterman algorithm using a new chip multiprocessor architecture with multiple Digital Signal Processors (DSP) on a single chip leading to high performance at low cost.