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 http://dna.cs.byu.edu/msa/.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Lloyd S,Snell QOdoi
10.1186/1471-2105-12-466subject
Has Abstractpub_date
2011-12-07 00:00:00pages
466issn
1471-2105pii
1471-2105-12-466journal_volume
12pub_type
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