Genetics Research International / 2012 / Article / Tab 4

Review Article

Mechanistic Roles of Noncoding RNAs in Lung Cancer Biology and Their Clinical Implications

Table 4

Examples of computational approaches used for ncRNA characterization.

MethodBrief descriptionReference

Secondary structure
MFOLDFolding prediction using a thermodynamic model, returning a structure of minimal free energy (MFE)[177]
RNAfold[103]
PKNOTSAlgorithm which finds optimal pseudoknotted RNA structures[178]
pknotsRGFinds the best RNA structure including the pseudoknot (based on MFE-model)[179, 180]

Sequence similarity search
INFERNALGenerates consensus RNA secondary structure, then searches for homologous RNAs, or creates new sequence- and structure-based multiple sequence alignments.[181]

Sequence-based alignments
RNAzPerforms de novo searches for RNA structure[182]
qRNAPredicts structured RNAs from sequence alignments (only works on pair-wise alignments) [183]
EvofoldFunctional RNA-structure identification in multiple sequence alignments [184]
DynalignA free energy minimization algorithm for joint alignment and secondary structure prediction [185]

Local searches
FOLDALIGNAlignment of RNA sequences and selection of subsets containing the most significant alignments. [186]
CMfinderFinds conserved RNA motifs in a set of unaligned sequences [187]

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