Protein Alignment Systolic Array Throughput Optimization

Protein comparison is gaining importance year after year since it has been demonstrated that biologists can find cor- relation between different species, or genetic mutations that can lead to cancer and genetic diseases. Protein sequence alignment is the most computational intensive task when performing protein comparison. In order to speed-up alignment, dedicated processors that can perform different computations in parallel have been designed. Among them, the best performance have been achieved using Systolic Arrays. However, when the Processing Elements of the Systolic Array have an internal loop, performance could be highly reduced. In this work we present an architectural strategy to address this problem applying pipeline interleaving; this strategy is applied to a Systolic Array for Smith Waterman algorithm that we designed. Results encourage the adoption of pipeline interleaving for parallel circuits with loop based Processing Elements. We demonstrate that important benefits in terms of higher operating frequency can be derived without so relevant costs as increased complexity, area and power required.