Abstract
BackgroundMultiple 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.ResultsWe 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.ConclusionsOur 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/.
Highlights
Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications
Reconfigurable computing allows a greater scale of parallelism using many finegrained custom processing elements that have a lowoverhead interconnect
Alignment quality with BRAliBase 2.1 is depicted in Figure 10 for MUDISC and several other MSA programs
Summary
Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Biologists and other researchers use multiple sequence alignment (MSA) as a fundamental analysis method to find similarities among nucleotide (DNA/RNA) or amino acid (protein) sequences. Producing timely results on large problems requires more efficient algorithms and the use of parallel computing resources. Reconfigurable computing hardware, such as Field-Programmable Gate Arrays (FPGAs), provides one approach to the acceleration of biological sequence alignment. Other acceleration methods typically encounter scaling problems that arise from the overhead of inter-process communication and from the lack of parallelism. Reconfigurable computing allows a greater scale of parallelism using many finegrained custom processing elements that have a lowoverhead interconnect
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