Predict structures formed by two molecules upon hybridization. +More...
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Collaboration diagram for Calculate Secondary Structures of two RNAs upon Dimerization:
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++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.
