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

## TL;DR

This paper explores adapting Darwin's hardware-accelerated DNA alignment algorithms for protein sequence alignment, proposing a multi-pass GACT variant that improves accuracy by 14% on average.

## Contribution

It demonstrates the feasibility of applying Darwin's algorithms to protein sequences and introduces a novel multi-pass GACT algorithm that enhances alignment accuracy.

## Key findings

- Multi-pass GACT improves alignment scores by 14% on average.
- Darwin's algorithms can be adapted for protein sequence alignment.
- The proposed method maintains efficient hardware implementation.

## Abstract

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.