Parallel Prefiltering for Accelerating HHblits on the Convey HC-1

Abstract

HHblits is a bioinformatics application for finding proteins with common ancestors. To achieve more sensitivity, the protein sequences of the query are not compared directly against the database protein sequences, but rather their Hidden Markov Models are compared. Thus, HHblits is very time-consuming and therefore needs to be accelerated. A multi-FPGA system such as the Convey HC-1 is a promising candidate to achieve acceleration. We present the design and implementation of a parallel coprocessor on the Convey HC-1 to accelerate HHblits after analyzing the application toward acceleration candidates. We achieve a speedup of 117.5× against a sequential implementation for FPGA-suitable data sizes per kernel and negligible speedup for the entire uniprot20 protein database against an optimized SSE implementation.