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Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute

  • Alexander ChurkinEmail author
  • Danny Barash
Open Access
Research Article
  • 766 Downloads
Part of the following topical collections:
  1. Advanced Signal Processing Techniques for Bioinformatics

Abstract

We introduce here for the first time the RNAMute package, a pattern-recognition-based utility to perform mutational analysis and detect vulnerable spots within an RNA sequence that affect structure. Mutations in these spots may lead to a structural change that directly relates to a change in functionality. Previously, the concept was tried on RNA genetic control elements called "riboswitches" and other known RNA switches, without an organized utility that analyzes all single-point mutations and can be further expanded. The RNAMute package allows a comprehensive categorization, given an RNA sequence that has functional relevance, by exploring the patterns of all single-point mutants. For illustration, we apply the RNAMute package on an RNA transcript for which individual point mutations were shown experimentally to inactivate spectinomycin resistance in Escherichia coli. Functional analysis of mutations on this case study was performed experimentally by creating a library of point mutations using PCR and screening to locate those mutations. With the availability of RNAMute, preanalysis can be performed computationally before conducting an experiment.

Keywords

Escherichia Coli Structural Change Information Technology Structural Analysis Functional Analysis 

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Copyright information

© Churkin and Barash 2006

Authors and Affiliations

  1. 1.Department of Computer ScienceBen-Gurion UniversityBeer-ShevaIsrael
  2. 2.Genome Diversity Center, Institute of EvolutionUniversity of HaifaIsrael

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