Some initial results on hardware BLAST acceleration with a reconfigurable architecture

The BLAST algorithm is the prevalent tool that is used by molecular biologists for DNA sequence matching and database search. In this work we demonstrate that with an appropriate reconfigurable architecture, BLAST performance can be improved with a single-chip solution 5 times over a specialized and optimized computer cluster, or 37 times over a single computer. These initial results account for I/O and are very encouraging for the development of a large scale, reconfigurable BLAST engine