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

Hua, Lei; Song, Yang; Kim, Namhee; Laing, Christian; Wang, Jason T. L.; Schlick, Tamar

doi:10.1371/journal.pone.0147097

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

Journal Article · Wed Jan 20 00:00:00 EST 2016 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0147097· OSTI ID:1627780

Hua, Lei ^[1]; Song, Yang ^[1]; Kim, Namhee ^[2]; Laing, Christian ^[1]; Wang, Jason T. L. ^[1]; Schlick, Tamar ^[2]

New Jersey Inst. of Technology, Newark, NJ (United States)
New York Univ. (NYU), NY (United States)

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/.

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Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: USDOE; National Science Foundation (NSF); National Institute of General Medical Sciences (NIGMS); State of New York

Grant/Contract Number:: AC02-98CH10886; IIS-0707571; GM100469; GM081410; TG-MCB080036N

OSTI ID:: 1627780

Journal Information:: PLoS ONE, Vol. 11, Issue 1; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 7 works

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