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.
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 ]