Advances in life sciences over the last few decades have lead to thegeneration of a huge amount of biological data. Computing research has become avital part in driving biological discovery where analysis and categorization ofbiological data are involved. String matching algorithms can be applied forprotein/gene sequence matching and with the phenomenal increase in the size ofstring databases to be analyzed, software implementations of these algorithmsseems to have hit a hard limit and hardware acceleration is increasingly beingsought. Several hardware platforms such as Field Programmable Gate Arrays(FPGA), Graphics Processing Units (GPU) and Chip Multi Processors (CMP) arebeing explored as hardware platforms. In this paper, we give a comprehensiveoverview of the literature on hardware acceleration of string matchingalgorithms, we take an FPGA hardware exploration and expedite the design timeby a design automation technique. Further, our design automation is alsooptimized for better hardware utilization through optimizing the number ofpeptides that can be represented in an FPGA tile. The results indicatesignificant improvements in design time and hardware utilization which arereported in this paper.
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