DASH: localising dynamic programming for order of magnitude faster, accurate sequence alignment

In this paper we present our genomic and proteomic sequence alignment algorithm, DASH, which results in order of magnitude speed improvement when compared to NCBI-BLAST 2.2.6, with superior sensitivity. Dynamic programming (DP) is the predominant contributor to search time for algorithms such as BLAST and FastA/P. Improving the efficiency of DP provides an opportunity to increase sensitivity, or significantly reduce search times and help offset the effects of the continuing exponential growth in database sizes. Specifically, for nucleotide searching we have demonstrated an order of magnitude speed improvement with significantly improved sensitivity, or alternatively moderate speed up with further sensitivity gains, depending on the parameters selected. Smith-Waterman complete DP is used as the sensitivity benchmark. Similar speed and sensitivity results are presented for protein searching. Since our algorithm is highly parallel, we have developed dedicated hardware which we will present in a companion paper, and a distributed version of our software (DDASH), which we expect to provide linear speedup on a cluster.