Accelerated Large-Scale Multiple Sequence Alignment with Reconfigurable Computing
SESSION: Doctoral Research Showcase I (Autotuning and Performance Engineering on Emerging and Scalable Systems)
EVENT TYPE: Doctoral Research Showcase
TIME: 2:06PM - 2:24PM
SESSION CHAIR: Sadaf R. Alam
ABSTRACT: Multiple Sequence Alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations according to Amdahl's Law. This work is the first known to accelerate the third stage of progressive alignment on reconfigurable hardware. We reduce subgroups of aligned sequences into discrete profiles before they are pairwise aligned on the accelerator. For a single pairwise alignment, a speedup of 300 has been demonstrated when compared to a 2.4 GHz Core2 processor (see Slide 2). Our parallel algorithm and architecture accelerates large-scale MSA with reconfigurable computing and allows researchers to solve the larger problems that confront biologists today.
Sadaf R. Alam (Chair) - Swiss National Supercomputing Centre