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

PloS One
Lei HuaTamar Schlick

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 ...Continue Reading

References

Oct 1, 1990·Computer Applications in the Biosciences : CABIOS·B A Shapiro, K Z Zhang
Jul 1, 1985·The Biochemical Journal·R Brimacombe, W Stiege
Dec 1, 1974·Proceedings of the National Academy of Sciences of the United States of America·S H KimA RICH
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Mar 21, 2002·Journal of Molecular Biology·David H Mathews, Douglas H Turner
Mar 23, 2002·Cell·Nancy A Woychik, Michael Hampsey
Apr 3, 2002·Nature Structural Biology·Jeffrey S KieftJennifer A Doudna
May 23, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Tao JiangKaizhong Zhang
Jun 26, 2003·Nucleic Acids Research·Huanwang YangEric Westhof
Sep 23, 2003·BMC Bioinformatics·Robert J Klein, Sean R Eddy
Nov 25, 2003·Bioinformatics·Lusheng Wang, Jianyun Zhao
Apr 1, 2004·Journal of the American Chemical Society·Terry A GoodyDavid G Norman
Apr 30, 2005·Nucleic Acids Research·Paul P GardnerStefan Washietl
Oct 6, 2005·Bioinformatics·Oranit DrorHaim Wolfson
Dec 24, 2005·RNA·Aurélie Lescoute, Eric Westhof
Sep 11, 1995·Nucleic Acids Research·D M LilleyP J Hagerman
Oct 20, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Matthias HöchsmannRobert Giegerich
Aug 19, 2007·Journal of Mathematical Biology·Michael SarverNeocles B Leontis
Oct 17, 2007·PLoS Computational Biology·Jakob H HavgaardJan Gorodkin
May 27, 2008·Nucleic Acids Research·Yen-Fu ChangChin Lung Lu
Jun 25, 2008·Annual Review of Biophysics·Stephen R Holbrook
Aug 15, 2008·BMC Bioinformatics·Mirela AndronescuAnne Condon
Oct 1, 2008·RNA·Mira AbrahamHaim J Wolfson
May 19, 2009·Journal of Molecular Biology·Christian Laing, Tamar Schlick
Jun 2, 2009·Nucleic Acids Research·Emidio Capriotti, Marc A Marti-Renom
Jun 17, 2009·Nucleic Acids Research·Craig L ZirbelNeocles B Leontis
Aug 8, 2009·Journal of Molecular Biology·Christian LaingTamar Schlick
May 28, 2010·RNA·Daniel P Aalberts, Nagarajan Nandagopal
May 29, 2010·Nucleic Acids Research·Chih-Wei WangChin Lung Lu
Aug 6, 2010·The Journal of Physical Chemistry. B·Sichun YangBenoît Roux
Oct 12, 2010·Bioinformatics·Ryan R RahrigCraig L Zirbel
Apr 26, 2011·Nucleic Acids Research·Anton I PetrovNeocles B Leontis
Jul 15, 2011·RNA·Eckart BindewaldBruce A Shapiro
Sep 9, 2011·Accounts of Chemical Research·Samuel E Butcher, Anna Marie Pyle

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Citations

Jul 7, 2019·Journal of Structural Biology·Christina Bergonzo, Alexander Grishaev
Nov 23, 2018·Journal of the American Chemical Society·Clark Templeton, Ron Elber

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Methods Mentioned

BETA
fluorescence resonance
NMR

Software Mentioned

SETTER
Junction - Explorer
SimulFold
RNAforester
Junction
- Explorer
RSmatch
FR3D
RNAView
ARTS

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