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RNAlib-2.4.17
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Predicting the Minimum Free Energy (MFE) and a corresponding (consensus) secondary structure. More...
Predicting the Minimum Free Energy (MFE) and a corresponding (consensus) secondary structure.
In a nutshell we provide two different flavors for MFE prediction:
Each of these flavors, again, provides two implementations to either compute the MFE based on
For the latter, a consensus secondary structure is predicted and our implementations compute an average of free energies for each sequence in the MSA plus an additional covariance pseudo-energy term.
The implementations for Backtracking MFE structures are generally agnostic with respect to whether local or global structure prediction is in place.
Collaboration diagram for Minimum Free Energy (MFE) Algorithms:Modules | |
| Global MFE Prediction | |
| Variations of the global Minimum Free Energy (MFE) prediction algorithm. | |
| Local (sliding window) MFE Prediction | |
| Variations of the local (sliding window) Minimum Free Energy (MFE) prediction algorithm. | |
| Backtracking MFE structures | |
| Backtracking related interfaces. | |
Files | |
| file | mfe.h |
| Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence data. | |
| file | mfe_window.h |
| Compute local Minimum Free Energy (MFE) using a sliding window approach and backtrace corresponding secondary structures. | |