SilentMutations (SIM): A tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs.

Computational Biology / methods Genome, Viral Hepacivirus / genetics Influenza A virus / genetics Nucleic Acid Conformation Point Mutation RNA, Viral / chemistry
Codon mutation Double-mutant RNA secondary structure RNA virus Silent mutation Virology Virus bioinformatics

Journal

Virus research
ISSN: 1872-7492
Titre abrégé: Virus Res
Pays: Netherlands
ID NLM: 8410979

Informations de publication

Date de publication:
15 01 2019
Historique:
received: 21 09 2018
revised: 30 10 2018
accepted: 09 11 2018
pubmed: 16 11 2018
medline: 23 1 2019
entrez: 16 11 2018
Statut: ppublish

Résumé

A single nucleotide change in the coding region can alter the amino acid sequence of a protein. In consequence, natural or artificial sequence changes in viral RNAs may have various effects not only on protein stability, function and structure but also on viral replication. In recent decades, several tools have been developed to predict the effect of mutations in structured RNAs such as viral genomes or non-coding RNAs. Some tools use multiple point mutations and also take coding regions into account. However, none of these tools was designed to specifically simulate the effect of mutations on viral long-range interactions. Here, we developed SilentMutations (SIM), an easy-to-use tool to analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. The tool can simulate disruptive and compensatory mutants of two interacting single-stranded RNAs. This allows a fast and accurate assessment of key regions potentially involved in functional long-range RNA-RNA interactions and will eventually help virologists and RNA-experts to design appropriate experiments. SIM only requires two interacting single-stranded RNA regions as input. The output is a plain text file containing the most promising mutants and a graphical representation of all interactions. We applied our tool on two experimentally validated influenza A virus and hepatitis C virus interactions and we were able to predict potential double mutants for in vitro validation experiments. The source code and documentation of SIM are freely available at github.com/desiro/silentMutations.

Identifiants

DOI: 10.1016/j.virusres.2018.11.005 PMID: 30439394 PMC: PMC7172452
pubmed: 30439394
pii: S0168-1702(18)30577-X
doi: 10.1016/j.virusres.2018.11.005
pmc: PMC7172452
pii:
doi:

Substances chimiques

RNA, Viral 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

135-141

Informations de copyright

Copyright © 2018. Published by Elsevier B.V.

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Auteurs

Daniel Desirò (D)

European Virus Bioinformatics Center, Jena, Germany; RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, Jena, Germany.

Martin Hölzer (M)

European Virus Bioinformatics Center, Jena, Germany; RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, Jena, Germany.

Bashar Ibrahim (B)

European Virus Bioinformatics Center, Jena, Germany; Chair of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University, Jena, Germany.

Manja Marz (M)

European Virus Bioinformatics Center, Jena, Germany; RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, Jena, Germany; Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany. Electronic address: manja@uni-jena.de.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › SilentMutations (SIM): A tool for analyzing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome viral › SilentMutations (SIM): A tool for analyzing...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Flaviviridae › Hepacivirus › SilentMutations (SIM): A tool for analyzing...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN de polarité négative › Orthomyxoviridae › Influenzavirus A › Virus de la grippe A › SilentMutations (SIM): A tool for analyzing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › SilentMutations (SIM): A tool for analyzing...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Mutation › Mutation ponctuelle › SilentMutations (SIM): A tool for analyzing...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN viral › SilentMutations (SIM): A tool for analyzing...