Performance and bandwidth optimization for biological sequence alignment

Abstract

Sequence alignment is an essential, but compute-intensive application in Bioinformatics. Hardware implementation speeds up this application by exploiting its inherent parallelism, where the performance of the hardware depends on its capability to align long sequences. In hardware terms, the length of a biological query sequence that can be aligned against a database sequence depends on the number of Processing Elements (PEs) available, which in turn depends on the amount of available hardware resources. In addition, the amount of available bandwidth to transfer the data processed by these PEs plays a significant role in defining the maximum performance. In this paper, we carry out a detailed performance and bandwidth analysis for biological sequence alignment and formulate theoretical performance boundaries for various cases. Further, we optimize the performance gain and memory bandwidth requirements and develop generalized equations for this optimization.