RNAlign2D – a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix

Abstract

Motivation The function of RNA molecules is mainly determined by their secondary structure. Addressing that issue requires creation of appropriate bioinformatic tools that enable alignment of multiple RNA molecules to determine functional domains and/or classify RNA families. The existing tools for RNA multiple alignment that use structural information are relatively slow. Therefore, providing a rapid tool for multiple structural alignment may improve classification of the known RNAs and reveal the function of the newly discovered ones. Results Here, we developed an extremely fast Python based RNAlign2D tool. It converts RNA sequence and structure to pseudo-amino acid sequence and uses customizable pseudo-amino acid substitution matrix to align RNA secondary structures and sequences using MUSCLE. It is suitable for RNAs containing modified nucleosides and/or pseudoknots. Our approach is compatible with virtually all protein aligners. Availability and implementation RNAlign2D is available from https://github.com/tomaszwozniakihg/rnalign2d. It has been tested on Linux and MacOSX. Supplementary information Supplementary data are available at Bioinformatics online.