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The Mercury BLASTN application is a hybrid hardware-software implementation of DNA-to-DNA sequence comparison. It presents an interface similar to that of NCBI BLASTN 2.2 (and indeed uses much of that package's source code internally) but has many changes "Under the hood" to support very large sequence comparisons. Much of Mercury BLASTN's speedup comes from effective use of custom-designed hardware circuits implemented on Field-Programmable Gate Arrays (FPGAs) that accelerate parts of the BLASTN computation. Additionally, the software part of the system is heavily multithreaded to enable parallel computation across multiple CPU cores.
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