thermodynamics and kinetics

minimum free energy, thermodynamic stability, kinetic folding

2D structure prediction

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

structure comparison

structure alignment, consensus shapes

miRNAs and target prediction

genome-wide prediction, target prediction and characterization, expression

RNA databases

RFam, miRBase, BRaliBase

modelling of RNA families

motif definition and motif search, structural clustering, covariance models

RNA gene prediction

from models, from 2D folding and comparison

RNA sequencing

deep sequencing of RNA transcripts

RNA 3D modelling

3D structure prediction, dynamics, simulations

computer tools

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