  Darwin is a genomics co-processor that achieved a 15000x acceleration on long
read assembly through innovative hardware and algorithm co-design. Darwins
algorithms and hardware implementation were specifically designed for DNA
analysis pipelines. This paper analyzes the feasibility of applying Darwins
algorithms to the problem of protein sequence alignment. In addition to a
behavioral analysis of Darwin when aligning proteins, we propose an algorithmic
improvement to Darwins alignment algorithm, GACT, in the form of a multi-pass
variant that increases its accuracy on protein sequence alignment. Concretely,
our proposed multi-pass variant of GACT achieves on average 14\% better
alignment scores.
