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/.