RNA inverse folding using Monte Carlo tree search

BMC Bioinformatics

Table 1 Existing tools and their ability to control GC-content and handle pseudoknot structures

Tools	Algorithm	GC content	Pseudoknot
RNAinverse [11]	Local search	No	No
RNA-SSD [12]	Stochastic local search	No	No
	and structure decomposition
INFO-RNA [13]	Dynamic programming	No	No
	and local search
NUPACK [14]	Minimization of ensemble	No	No
	defect and structure
	decomposition
RNAexinv [35]	Simulated annealing	No	No
Frnakenstein [15]	Genetic algorithm	No	No
EteRNABot [36]	Downhill simplex algorithm	No	No
ERD [16]	Evolutionary algorithm	No	No
	and structure
	decomposition
RNAifold [19]	Constraint programming	Yes	No
	and structure
	decomposition
IncaRNAtion [18]	Weighted sampling	Yes	No
	algorithm and
	local search
MODENA [17]	Multi-objective	Yes	Yes
	genetic algorithm
antaRNA [7, 30]	Ant colony optimization	Yes	Yes
Enzymer [37]	Adaptive weighted	No	Yes
	sampling
MCTS-RNA	Monte Carlo tree search	Yes	Yes

ISSN: 1471-2105