▼Free energy evaluation | Secondary structure and loop free energy evaluation |
Process and evaluate individual loops | |
▼The RNA folding grammar | The RNA folding grammar as implemented in RNAlib |
Fine-tuning of the implemented models | Functions and data structures to fine-tune the implemented secondary structure evaluation model |
▼Energy parameters | All relevant functions to retrieve and copy pre-calculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s) |
▼Reading/Writing Energy Parameter Sets from/to File | Read and Write energy parameter sets from and to text files |
Converting Energy Parameter Files | Convert energy parameter files into the latest format |
▼Extending the folding grammar with additional domains | This module covers simple and straight-forward extensions to the RNA folding grammar |
Unstructured domains | Add and modify unstructured domains to the RNA folding grammar |
Structured domains | Add and modify structured domains to the RNA folding grammar |
▼Constraining the RNA folding grammar | This module provides general functions that allow for an easy control of constrained secondary structure prediction and evaluation |
Hard constraints | This module covers all functionality for hard constraints in secondary structure prediction |
Soft constraints | Functions and data structures for secondary structure soft constraints |
▼Minimum Free Energy (MFE) algorithms | Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence data |
MFE Consensus Structures for Sequence Alignment(s) | |
Calculating MFE representatives of a Distance Based Partitioning | Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures |
MFE Structures of single Nucleic Acid Sequences | This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences |
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 |
Local MFE structure Prediction and Z-scores | |
▼Partition function and equilibrium properties | Compuate the partition function and various equilibrium properties derived from it |
Partition Function and Base Pair Probabilities for Sequence Alignment(s) | |
Calculate Partition Functions of a Distance Based Partitioning | Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures |
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 |
Partition functions for locally stable secondary structures | |
▼Suboptimals and representative structures | Sample and enumerate suboptimal secondary structures from RNA sequence data |
Suboptimal structures sensu Stiegler et al. 1984 / Zuker et al. 1989 | |
Suboptimal structures within an energy band arround the MFE | |
▼Structure sampling from the ensemble | |
Stochastic Backtracking of Consensus Structures from Sequence Alignment(s) | |
Stochastic Backtracking of Structures from Distance Based Partitioning | Contains functions related to stochastic backtracking from a specified distance class |
Compute the structure with maximum expected accuracy (MEA) | |
Compute the centroid structure | |
▼RNA-RNA interaction | Predict structures formed by two molecules upon hybridization |
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 |
▼Locally stable structures | |
Local MFE structure Prediction and Z-scores | |
Partition functions for locally stable secondary structures | |
Local MFE consensus structures for Sequence Alignments | |
▼Comparative structure prediction | Compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments |
MFE Consensus Structures for Sequence Alignment(s) | |
Partition Function and Base Pair Probabilities for Sequence Alignment(s) | |
Stochastic Backtracking of Consensus Structures from Sequence Alignment(s) | |
Local MFE consensus structures for Sequence Alignments | |
▼Classified Dynamic Programming variants | |
▼Distance based partitioning of the Secondary Structure Space | Compute Thermodynamic properties for a Distance Class Partitioning of the Secondary Structure Space |
Calculating MFE representatives of a Distance Based Partitioning | Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures |
Calculate Partition Functions of a Distance Based Partitioning | Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures |
Stochastic Backtracking of Structures from Distance Based Partitioning | Contains functions related to stochastic backtracking from a specified distance class |
Compute the Density of States | |
Inverse Folding (Design) | RNA sequence design |
▼Refolding paths between secondary structues | |
Direct refolding paths between two secondary structures | Heuristics to explore direct, optimal (re-)folding paths between two secondary structures |
▼Experimental structure probing data | Include experimental structure probing data to guide structure predictions |
SHAPE reactivity data | Incorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints |
Generate soft constraints from data | Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments |
▼Ligands binding to RNA structures | Simple extensions to model ligand binding to RNA structures |
Ligands binding to unstructured domains | Add ligand binding to loop regions using the Unstructured domains feature |
Incorporating ligands binding to specific sequence/structure motifs using soft constraints | Ligand binding to specific hairpin/interior loop like motifs using the Soft constraints feature |
▼Complex structured modules | |
G-quadruplexes | Various functions related to G-quadruplex computations |
▼Data Structures and Preprocessor Macros | All datastructures and typedefs shared among the Vienna RNA Package can be found here |
The Fold Compound | This module provides interfaces that deal with the most basic data structure used in structure predicting and energy evaluating function of the RNAlib |
The Dynamic Programming Matrices | This module provides interfaces that deal with creation and destruction of dynamic programming matrices used within the RNAlib |
▼Utilities | |
Parsing, converting, and comparing sequences | |
Parsing, converting, comparing secondary structures | |
Utilities for sequence alignments | |
Functions to Read/Write several File Formats for RNA Sequences, Structures, and Alignments | Functions dealing with file formats for RNA sequences, structures, and alignments |
Functions for Creating RNA Secondary Structures Plots, Dot-Plots, and More | |
Functions to convert between various units | |