accelerated large-scale multiple sequence alignment加速大规模多序列比对.pdfVIP

Lloyd and Snell BMC Bioinformatics 2011, 12:466 /1471-2105/12/466 RESEARCH ARTICLE Open Access Accelerated large-scale multiple sequence alignment * Scott Lloyd and Quinn O Snell Abstract 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 /msa/. Background scores only. Since this stage is easily parallelized, it has Biologists and other researchers use multiple sequence traditionally been the focus of parallelization efforts; alignment (MSA) as a fundamental analysis method to however, speedup is limited without accelerating the fol- find similarities among nucleotide (DNA/RNA) or amino lowing stages. The second stage of MSA groups the acid (protein) sequences. The compute time for an opti- most similar sequences together using the similarity mal MSA grows exponentia