Harnessing machine translation methods for sequence alignment

The sequence alignment problem is one of the most fundamental problems in bioinformatics and a plethora of methods were devised to tackle it. Here we introduce BetaAlign, a novel methodology for aligning sequences using a natural language processing (NLP) approach. BetaAlign accounts for the possible variability of the evolutionary process among different datasets by using an ensemble of transformers, each trained on millions of samples generated from a different evolutionary model. Our approach leads to outstanding alignment accuracy, often outperforming commonly used methods, such as MAFFT, DIALIGN, ClustalW, T-Coffee, and MUSCLE. Notably, the utilization of deep-learning techniques for the sequence alignment problem brings additional advantages, such as automatic feature extraction that can be leveraged for a variety of downstream analysis tasks.