Multi-objective genetic algorithm for pseudoknotted RNA sequence design.

Frontiers in Genetics
Akito Taneda

Abstract

RNA inverse folding is a computational technology for designing RNA sequences which fold into a user-specified secondary structure. Although pseudoknots are functionally important motifs in RNA structures, less reports concerning the inverse folding of pseudoknotted RNAs have been done compared to those for pseudoknot-free RNA design. In this paper, we present a new version of our multi-objective genetic algorithm (MOGA), MODENA, which we have previously proposed for pseudoknot-free RNA inverse folding. In the new version of MODENA, (i) a new crossover operator is implemented and (ii) pseudoknot prediction methods, IPknot and HotKnots, are used to evaluate the designed RNA sequences, allowing us to perform the inverse folding of pseudoknotted RNAs. The new version of MODENA with the new crossover operator was benchmarked with a dataset composed of natural pseudoknotted RNA secondary structures, and we found that MODENA can successfully design more pseudoknotted RNAs compared to the other pseudoknot design algorithm. In addition, a sequence constraint function newly implemented in the new version of MODENA was tested by designing RNA sequences which fold into the pseudoknotted structure of a hepatitis delta virus ribozyme; as a ...Continue Reading

Citations

Jan 11, 2014·Bioinformatics·Ali Esmaili-TaheriMorteza Mohammad-Noori
Sep 9, 2015·ACS Combinatorial Science·Hosna JabbariCarlo Montemagno
Nov 20, 2015·BMC Bioinformatics·Robert KleinkaufMartin Mann
Aug 1, 2013·Mathematical Biosciences·Fenix W D HuangChristian M Reidys
May 18, 2016·Nucleic Acids Research·Matan Drory RetwitzerDanny Barash
Jan 4, 2017·Briefings in Bioinformatics·Alexander ChurkinDanny Barash
Feb 14, 2017·Journal of the American Chemical Society·Brian R WolfeNiles A Pierce
Sep 5, 2017·Sensors·Sven FindeißPeter F Stadler
Oct 21, 2014·ACS Synthetic Biology·Brian R Wolfe, Niles A Pierce

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Software Mentioned

RNAinverse
INFO
RNAfold
NSGA2
MOGA
SSD
CentOS
+ IPknot
Inv
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