RNAlib-2.3.1
RNA-RNA interaction

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

+ Collaboration diagram for RNA-RNA interaction:

Modules

 MFE Structures of two hybridized Sequences
 MFE version of cofolding routines This file includes (almost) all function declarations within the RNAlib that are related to MFE Cofolding... This also includes the Zuker suboptimals calculations, since they are implemented using the cofold routines.
 
 Partition Function for two hybridized Sequences
 Partition Function Cofolding.
 
 Partition Function for two hybridized Sequences as a stepwise Process
 RNA-RNA interaction as a stepwise process.
 

Files

file  cofold.h
 MFE implementations for RNA-RNA interaction.
 
file  duplex.h
 Functions for simple RNA-RNA duplex interactions.
 
file  part_func_co.h
 Partition function for two RNA sequences.
 
file  part_func_up.h
 Implementations for accessibility and RNA-RNA interaction 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 allows one 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.