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

IMPACT: Interval-based Multi-pass Proteomic Alignment with Constant Traceback