Table 4.

Examples of computational approaches used for ncRNA characterization.

Method	Brief description	Reference
Secondary structure
MFOLD	Folding prediction using a thermodynamic model, returning a structure of minimal free energy (MFE)	[177]
RNAfold		[103]
PKNOTS	Algorithm which finds optimal pseudoknotted RNA structures	[178]
pknotsRG	Finds the best RNA structure including the pseudoknot (based on MFE-model)	[179, 180]
Sequence similarity search
INFERNAL	Generates consensus RNA secondary structure, then searches for homologous RNAs, or creates new sequence- and structure-based multiple sequence alignments.	[181]
Sequence-based alignments
RNAz	Performs de novo searches for RNA structure	[182]
qRNA	Predicts structured RNAs from sequence alignments (only works on pair-wise alignments)	[183]
Evofold	Functional RNA-structure identification in multiple sequence alignments	[184]
Dynalign	A free energy minimization algorithm for joint alignment and secondary structure prediction	[185]
Local searches
FOLDALIGN	Alignment of RNA sequences and selection of subsets containing the most significant alignments.	[186]
CMfinder	Finds conserved RNA motifs in a set of unaligned sequences	[187]