RNA structure prediction
Posts tagged “RNA structure prediction”.
RNAplfold tutorial: accessibility in long RNAs
How to compute the accessibility of a region with RNAplfold in the ViennaRNA Package, i.e. the probability that a stretch of nucleotides is unpaired, how to read the _lunp file, how to choose the...
SHAPE and chemical probing tutorial: folding with reactivities in RNAfold
How SHAPE reactivities go into RNAfold, what the three methods in ViennaRNA do with them, and what probing data change in a prediction and what they do not. Worked example with yeast tRNA-Phe, all commands included.
Conserved RNA regulatory switches in living cells
Transcriptome-scale ensemble mapping combined with covariation analysis reveals conserved RNA thermometers in bacteria and regulatory 5' UTR switches in human cells.
Predicting RNA structures from sequence and probing data
This review explains how classical thermodynamic RNA folding models can be improved with chemical probing data, and why that combination remains one of the most reliable routes to biologically useful structure prediction.
SHAPE-directed RNA folding with ViennaRNA: reactivities as soft constraints
This paper shows how SHAPE-guided RNA folding is implemented in the ViennaRNA Package, comparing three widely used strategies for turning nucleotide reactivities into soft constraints that improve thermodynamic...