topics

minimum free energy, thermodynamic stability, kinetic folding

RNA folding, optimal and suboptimal structures, base pair probabilities, abstract shape analysis

structure alignment, consensus shapes

genome-wide prediction, target prediction and characterization, expression

RFam, miRBase, BRaliBase

motif definition and motif search, structural clustering, covariance models

from models, from 2D folding and comparison

deep sequencing of RNA transcripts

3D structure prediction, dynamics, simulations

Vienna RNA package, RNAshapes, RNAz, RNAforester, Infernal, s2s, Assemble and more