RNAMute: RNA secondary structure mutation analysis tool

Alexander Churkin, Ornit Elgad, Oshrat Petgho, Danny Barash

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations

Abstract

RNAMute is an interactive web tool written in Java that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their distances from the wildtype 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, 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 tables lists all single point mutations belonging to that category. Selecting a mutation displays a graphical picture of the single point mutation and the wildtype, and includes basic information such as associated energies, representations, distances. RNAMute is a user friendly tool that can be used to predict single point mutations leading to conformational rearrangements in the secondary structure of RNAs.

Original languageEnglish
Title of host publication2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts
Pages139-140
Number of pages2
DOIs
StatePublished - 1 Dec 2005
Event2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts - Stanford, CA, United States
Duration: 8 Aug 200511 Aug 2005

Publication series

Name2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts

Conference

Conference2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts
Country/TerritoryUnited States
CityStanford, CA
Period8/08/0511/08/05

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