Many moons ago, I worked on an FPGA-based platform that was among several research projects targeted at the Genome Project. The general idea was to offload BLAST-style sequence alignment to purpose-compiled FPGAs, such that sequencing across the entire dataset could be performed in order of magnitude less time. It really wasn't all that complex (I just implemented Smith-Waterman directly, as a demonstration), only intended to perform fuzzy matches at Gbps speeds to winnow the working dataset down to a size more palatable to a desktop workstation.<p>My understanding is that all these projects (mine included) were cast adrift when the funding for them evaporated in the post-9/11 climate. In the intervening years, I was aware that Perl was being picked rapidly at the Genomics labs in the nearby university hospital (i.e. since we never delivered them the FPGA platform), and I'm happy to read Perl has risen to fill this niche.