QuickProbs 2: towards rapid construction of high-quality alignments of large protein families

TL;DR

QuickProbs 2 is a fast and accurate multiple sequence alignment algorithm designed for large protein families, outperforming existing methods in accuracy and scalability, especially with hundreds of sequences.

Contribution

The paper introduces QuickProbs 2, a novel alignment algorithm that combines probabilistic models with innovative refinement and selective consistency for high-quality, scalable alignments.

Findings

Outperforms Clustal Omega on large protein families

Superior accuracy on small sets compared to other methods

Significantly faster than full consistency approaches

Abstract

Increasing size of sequence databases caused by the development of high throughput sequencing, poses multiple alignment algorithms to face one of the greatest challenges yet. As we show, well-established techniques employed for increasing alignment quality, i.e., refinement and consistency, are ineffective when large protein families are of interest. We present QuickProbs 2, an algorithm for multiple sequence alignment. Based on probabilistic models, equipped with novel column-oriented refinement and selective consistency, it offers outstanding accuracy. When analysing hundreds of sequences, QuickProbs 2 is significantly better than Clustal Omega, the previous leader for processing numerous protein families. In the case of smaller sets, for which consistency-based methods are the best performing, QuickProbs 2 is also superior to the competitors. Due to computational scalability of selective consistency and utilisation of massively parallel architectures, presented algorithm is comparable to Clustal Omega in terms of execution time, and orders of magnitude faster than full consistency approaches, like MSAProbs or PicXAA. All these make QuickProbs 2 a useful tool for aligning families ranging from few, to hundreds of proteins. QuickProbs 2 is available at https://github.com/refresh-bio/QuickProbs.