rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling.

The multiple sequence alignment (MSA) is the entry point of many RNA structure modeling tasks, such as prediction of RNA secondary structure (rSS) and contacts. However, there are few automated programs for generating high quality MSAs of target RNA molecules. We have developed rMSA, a hierarchical pipeline for sensitive search and accurate alignment of RNA homologs for a target RNA. On a diverse set of 365 non-redundant RNA structures, rMSA significantly outperforms an existing MSA generation method (RNAcmap) by approximately 20% and 5% higher F1-scores for rSS and long-range contact prediction, respectively. rMSA is available at https://zhanggroup.org/rMSA/ and https://github.com/pylelab/rMSA.