Calculate Secondary Structures of two RNAs upon Dimerization
RNA Secondary Structure Prediction

Predict structures formed by two molecules upon hybridization. More...

Collaboration diagram for Calculate Secondary Structures of two RNAs upon Dimerization:

## Modules

| MFE Structures of two hybridized Sequences
| Partition Function for two hybridized Sequences
| Partition Function Cofolding.
| Partition Function for two hybridized Sequences as a stepwise Process
| Partition Function Cofolding as a stepwise process.

## Detailed Description

Predict structures formed by two molecules upon hybridization.

The function of an RNA molecule often depends on its interaction with other RNAs. The following routines therefore allow to predict structures formed by two RNA molecules upon hybridization.
One approach to co-folding two RNAs consists of concatenating the two sequences and keeping track of the concatenation point in all energy evaluations. Correspondingly, many of the cofold() and co_pf_fold() routines below take one sequence string as argument and use the the global variable cut_point to mark the concatenation point. Note that while the RNAcofold program uses the '&' character to mark the chain break in its input, you should not use an '&' when using the library routines (set cut_point instead).
In a second approach to co-folding two RNAs, cofolding is seen as a stepwise process. In the first step the probability of an unpaired region is calculated and in a second step this probability of an unpaired region is multiplied with the probability of an interaction between the two RNAs. This approach is implemented for the interaction between a long target sequence and a short ligand RNA. Function pf_unstru() calculates the partition function over all unpaired regions in the input sequence. Function pf_interact(), which calculates the partition function over all possible interactions between two sequences, needs both sequence as separate strings as input.