A Hybrid Flow For Multiple Sequence Alignment With A Blastn Based Pairwise Alignment Processor

In this paper, we design a special-purpose processor for pairwise alignment and propose to integrate this design into a Multiple Sequence Alignment (MSA) flow. The processor is based on a modified algorithm of Banded Two-Hit Basic Local Alignment Search Tool for Nucleotides (MB2-BLASTn). In the new hybrid MSA flow, our MB2-BLASTn processor is used to find pairwise alignment first. Then the results are sent to CPUs for tree-building and progressive alignment. Since the pairwise alignment takes about 90% of total computing time in the original software flow, 100X speedup achieved by MB2-BLASTn can greatly improve the speed of MSA.