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/.
Highlights
RNA secondary structures are composed of double-stranded segments such as helices connected to single-stranded regions such as junctions and hairpin loops
RNA junctions exist in numerous RNA molecules; they play important roles in a wide variety of biochemical activities such as self-cleavage of the hammerhead ribozyme [11], the recognition of the binding pocket domain by purine riboswitches [12] and the translation initiation of the hepatitis C virus at the internal ribosome entry site [13]
We have presented a novel method (CHSalign) capable of producing an optimal alignment between two input RNA secondary (2D) structures with coaxial helical stacking (CHS), based on our previously developed Junction-Explorer [25] and RNAJAG [4]
Summary
RNA secondary structures are composed of double-stranded segments such as helices connected to single-stranded regions such as junctions and hairpin loops. These structural elements serve as building blocks in the design of diverse RNA molecules with various functions. RNA junctions are important structural elements due to their ability to orient many parts of the RNA molecule [4]. An RNA junction, known as a multi-branch loop, forms when more than two helical segments are brought together [5,6,7,8,9,10]. A junction database, called RNAJunction, has been established, which contains junctions of all known degrees of branching [5]
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