ReAlign-P: a vertical iterative realignment method for protein multiple sequence alignment

Reliable protein multiple sequence alignment (MSA) is essential for downstream biomedical research and directly impacts the accuracy of analytical results. However, protein sequences often exhibit low similarity and complex alignment patterns, and existing general alignment tools frequently fall short in terms of accuracy. Many current realignment methods are outdated, suffering from issues such as code obsolescence and inadequate precision. As a result, there is a pressing need for realignment methods that can better address these challenges.

This study introduces ReAlign-P, a realignment tool designed specifically for protein MSA. ReAlign-P first divides the initial alignment into three regions and applies a novel vertical iterative realignment strategy to optimize the more conserved middle region. This method is by default compatible with MUSCLE5 for realignment, leading to a significant improvement in accuracy. We evaluated initial alignments generated using 10 different MSA parameter configurations across four protein benchmark datasets. The results demonstrate that ReAlign-P consistently outperforms or matches the quality of the initial alignments in all cases. In contrast, RASCAL-the only other currently functional protein realignment tool-sometimes even reduces alignment quality. ReAlign-P not only delivers more substantial improvements but also exhibits greater stability, effectively addressing the gap in available protein realignment tools.

The source code and test data for ReAlign-P are available on GitHub (https://github.com/malabz/ReAlign-P).