Multi-objective optimization for RNA design with multiple target secondary structures

BMC Bioinformatics
Akito Taneda

Abstract

RNAs are attractive molecules as the biological parts for synthetic biology. In particular, the ability of conformational changes, which can be encoded in designer RNAs, enables us to create multistable molecular switches that function in biological circuits. Although various algorithms for designing such RNA switches have been proposed, the previous algorithms optimize the RNA sequences against the weighted sum of objective functions, where empirical weights among objective functions are used. In addition, an RNA design algorithm for multiple pseudoknot targets is currently not available. We developed a novel computational tool for automatically designing RNA sequences which fold into multiple target secondary structures. Our algorithm designs RNA sequences based on multi-objective genetic algorithm, by which we can explore the RNA sequences having good objective function values without empirical weight parameters among the objective functions. Our algorithm has great flexibility by virtue of this weight-free nature. We benchmarked our multi-target RNA design algorithm with the datasets of two, three, and four target structures and found that our algorithm shows better or comparable design performances compared with the previo...Continue Reading

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Citations

Mar 30, 2017·ACS Synthetic Biology·Irene Otero-Muras, Julio R Banga
Apr 28, 2017·Bioinformatics·Stefan HammerSven Findeiß
Apr 27, 2019·BMC Bioinformatics·Stefan HammerYann Ponty
Nov 8, 2017·BMC Bioinformatics·Xiufeng YangKoji Tsuda
Apr 4, 2021·International Journal of Molecular Sciences·Akito Taneda, Kengo Sato
Jun 3, 2021·Algorithms for Molecular Biology : AMB·Fenix W HuangChristian M Reidys
Jul 13, 2019·ACS Synthetic Biology·Michelle J WuRhiju Das

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Methods Mentioned

BETA
interaction prediction

Software Mentioned

MODENA
RNAstructure
RNAinverse
RNAtabupath
IPknot
Fold
RNAfold
GA
accessFindPath py
centroidfold

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