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High-Performance Direct Pairwise Comparison of Large Genomic Sequences

Category: Data Management, Desktops, Laptops and OS

Overview Many applications in Comparative Genomics lend themselves to implementations that take advantage of common high-performance features in modern microprocessors. However, the common suggestion that a data-parallel, multithreaded, or high-throughput implementation is possible often ignores the complexity of actually creating such software. This paper presents a data-parallel algorithm for a classic comparative genomics algorithm, the dot plot, along with a multiprocessor extension. For large genomic comparisons, these new algorithms achieve speedups of up to 14.4x over the sequential version. This speedup introduces the opportunity of performing full pairwise comparisons on entire genomes on a much larger scale than previously possible.

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Publisher: Indiana University
File Format: PDF
Date Published: Oct 22, 2008
Format: White Papers
Topics: Microprocessors, High Performance Computing

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