CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

TL;DR

CHSalign is a web-based tool that improves the alignment of RNA secondary structures with coaxial helical stacking motifs by building on Junction-Explorer and RNAJAG, offering higher accuracy for structures with similar junctions.

Contribution

The paper introduces CHSalign, a novel RNA secondary structure alignment method that incorporates coaxial stacking predictions and junction topology modeling for improved accuracy.

Findings

CHSalign outperforms existing tools in aligning RNA structures with CHS motifs.

The method achieves high scores for similar junctions and stacking patterns.

The web server implementation makes the tool accessible for researchers.

Abstract

RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS) motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.