# Getting Started

Here you find some more or less elaborate tutorials and manuals on how to use our software.

Note

The tutorials provided below are mostly taken from A short Tutorial on RNA Bioinformatics The ViennaRNA Package and related Programs. Since they have not been updated for quite some time, some of the described features may not work as expected and novel features of our programs may not be mentioned.

We will be working on extending this part of the documentation in the future.

## Global RNA Secondary Structure Prediction

Several tools for structure prediction of single RNA sequences are available within the `ViennaRNA Package`, each with its own special subset of implemented algorithms.

- The Program `RNAfold`
- The Program `RNApvmin`
- The Program `RNAsubopt`

## Consensus Structure Prediction

Consensus structures can be predicted by a modified version of the secondary structure prediction algorithm that takes as input a set of aligned sequences instead of a single sequence.

Sequence co-variations are a direct consequence of RNA base pairing rules and can be deduced to alignments. RNA helices normally contain only 6 out of the 16 possible combinations: the Watson-Crick pairs `GC`, `CG`, `AU`, `UA`, and the somewhat weaker wobble pairs `GU` and `UG`. Mutations in helical regions therefore have to be correlated. In particular we often find compensatory mutations where a mutation on one side of the helix is compensated by a second mutation on the other side, e.g. a `CG` pair changes into a `UA` pair. Mutations where only one pairing partner changes (such as `CG` to `UG` are termed consistent mutations.

The energy function consists of the mean energy averaged over the sequences, plus a covariance term that favors pairs with consistent and compensatory mutations and penalizes pairs that cannot be formed by all structures. For details see Hofacker et al. [2002] and Bernhart et al. [2008].

- The Program `RNAalifold`

## RNA-RNA interaction

A common problem is the prediction of binding sites between two RNAs, as in the case of miRNA-mRNA interactions. Following tools of the `ViennaRNA Package` can be used to calculate base pairing probabilities.

- The Program `RNAcofold`
- The Program `RNAduplex`

## Plotting Structures

- The Program `RNAplot`

## RNA Design

- The Program `RNAinverse`
- The Program `switch.pl`

## RNA folding kinetics

RNA folding kinetics describes the dynamical process of how a RNA molecule approaches to its unique folded biological active conformation (often referred to as the native state) starting from an initial ensemble of disordered conformations e.g. the unfolded open chain. The key for resolving the dynamical behavior of a folding RNA chain lies in the understanding of the ways in which the molecule explores its astronomically large free energy landscape, a rugged and complex hyper-surface established by all the feasible base pairing patterns a RNA sequence can form. The challenge is to understand how the interplay of formation and break up of base pairing interactions along the RNA chain can lead to an efficient search in the energy landscape which reaches the native state of the molecule on a biologically meaningful time scale.

- The Program `RNA2Dfold`
- The Programs `barriers` and `treekin`

## Other Utilities

- Utilities