Scalability Studies of the BLASTn Scan and Ungapped Extension Functions

BLASTn is a ubiquitous and important tool used for large scale DNA analysis. As such, it is a good candidate for acceleration with FPGAs. The aim of this paper is two-fold. First, building upon our prior BLAST work we describe a design composed of multiple cores that can be scaled in two dimensions. The ungapped extension and a second dimension are new in this work. Second, we use this non-trivial example to explore spatially scalable designs. To provide the ability to move the design to a future generation chip, a mathematical model of performance that incorporates all of the system design parameters and the user´s preference (high throughput vs low latency) is developed. We demonstrate here that the model correctly predicts the optimal ratio between the two dimensions on a Xilinx Virtex-4 and measures four to five times faster performance figures as compared to a state of the art general purpose processor.