Accelerated Large-Scale Multiple Sequence Alignment

Scott Lloyd, Quinn O. Snell
Computer Science Department, Brigham Young University, Provo, UT 84602, USA
BMC Bioinformatics, 12:466, 2011


   title={Accelerated Large-Scale Multiple Sequence Alignment},

   author={Lloyd, S. and Snell, Q.O.},

   journal={BMC bioinformatics},





   publisher={BioMed Central Ltd}


BACKGROUND: 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. RESULTS: We reduce subgroups of aligned sequences into discrete profiles before they are pairwise aligned on the accelerator. Using an FPGA accelerator, an overall speedup of up to 150 has been demonstrated on a large data set when compared to a 2.4 GHz Core2 processor. CONCLUSIONS: Our parallel algorithm and architecture accelerates large-scale MSA with reconfigurable computing and allows researchers to solve the larger problems that confront biologists today. Program source is available from http://dna.cs.byu.edu/msa/.
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