RNAmute: RNA secondary structure mutation analysis tool.

BMC Bioinformatics
Alexander Churkin, Danny Barash

Abstract

RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with respect to the wild type predicted structure. The secondary structure predictions are performed using the Vienna RNA package. Several alternatives are used for the categorization of single point mutations: Vienna's RNAdistance based on dot-bracket representation, as well as tree edit distance and second eigenvalue of the Laplacian matrix based on Shapiro's coarse grain tree graph representation. Selecting a category in each one of the processed tables lists all single point mutations belonging to that category. Selecting a mutation displays a graphical drawing of the single point mutation and the wild type, and includes basic information such as associated energies, representations and distances. RNAMute can be used successfully with very little previous experience and without choosing any parameter value alongside the initial RNA sequence. The package runs under LINUX operating system. RNAMute is a user friendly tool that can be used to predict single point mutations leading to conformational rearrangements in the secondary...Continue Reading

References

Aug 1, 1988·Computer Applications in the Biosciences : CABIOS·B A Shapiro
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Oct 1, 1989·Computers and Biomedical Research, an International Journal·S Y LeJ V Maizel
Apr 12, 1994·Proceedings of the National Academy of Sciences of the United States of America·K A LeCuyer, D M Crothers
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Apr 3, 2001·Science·M M YusupovH F Noller
Dec 20, 2002·Nucleic Acids Research·Jeff M Zimmerman, L James Maher
Jun 26, 2003·Nucleic Acids Research·Michael Zuker
Jun 26, 2003·Nucleic Acids Research·Ivo L Hofacker
Nov 7, 2003·Nucleic Acids Research·Danny Barash
Apr 22, 2008·Nucleic Acids Research·Andreas R GruberIvo L Hofacker
Apr 23, 2008·Current Protocols in Bioinformatics·Ivo L Hofacker

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Citations

Mar 23, 2011·Briefings in Bioinformatics·Danny Barash, Alexander Churkin
Apr 12, 2011·Nucleic Acids Research·Alexander ChurkinDanny Barash
May 21, 2011·Nucleic Acids Research·Edmund LamJérôme Waldispühl
Sep 8, 2006·BMC Bioinformatics·Wenjie ShuShengqi Wang
Apr 12, 2008·BMC Bioinformatics·Wenjie ShuShengqi Wang
Feb 11, 2009·Algorithms for Molecular Biology : AMB·Tor IvryDanny Barash
Sep 11, 2012·Algorithms for Molecular Biology : AMB·Iddo AviramDanny Barash
Apr 21, 2009·Pharmacogenomics·Grace S Y PangCaroline G L Lee
Jun 28, 2013·Briefings in Bioinformatics·Michiaki Hamada
Feb 5, 2015·BMC Genomics·Shermin PeiMichelle M Meyer
Jan 27, 2015·Nucleic Acids Research·Meredith CorleyAlain Laederach
Sep 6, 2007·Journal of Mathematical Biology·Ariane Machado-LimaAlan Mitchell Durham
Apr 30, 2011·Molecular Endocrinology·Yvonne BockmühlDietmar Spengler
Jan 15, 2013·Human Mutation·Radhakrishnan SabarinathanJan Gorodkin
Nov 14, 2012·Computational Biology and Chemistry·Alexander ChurkinDanny Barash

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Software Mentioned

RNAMute
RNAdistance
Vienna RNA
mfold
Vienna
Vienna RNA package
runRnaMute
Progs
b2Shapiro
single

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