RNAlib-2.3.1
Modules
Here is a list of all modules:
[detail level 1234]
 Free energy evaluationSecondary structure and loop free energy evaluation
 Process and evaluate individual loops
 The RNA folding grammarThe RNA folding grammar as implemented in RNAlib
 Fine-tuning of the implemented modelsFunctions and data structures to fine-tune the implemented secondary structure evaluation model
 Energy parametersAll 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 FileRead and Write energy parameter sets from and to text files
 Converting Energy Parameter FilesConvert energy parameter files into the latest format
 Extending the folding grammar with additional domainsThis module covers simple and straight-forward extensions to the RNA folding grammar
 Unstructured domainsAdd and modify unstructured domains to the RNA folding grammar
 Structured domainsAdd and modify structured domains to the RNA folding grammar
 Constraining the RNA folding grammarThis module provides general functions that allow for an easy control of constrained secondary structure prediction and evaluation
 Hard constraintsThis module covers all functionality for hard constraints in secondary structure prediction
 Soft constraintsFunctions and data structures for secondary structure soft constraints
 Minimum Free Energy (MFE) algorithmsCompute 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 PartitioningCompute 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 SequencesThis module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences
 MFE Structures of two hybridized SequencesMFE 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 propertiesCompuate 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 PartitioningCompute 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 SequencesPartition Function Cofolding
 Partition Function for two hybridized Sequences as a stepwise ProcessRNA-RNA interaction as a stepwise process
 Partition functions for locally stable secondary structures
 Suboptimals and representative structuresSample 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 PartitioningContains functions related to stochastic backtracking from a specified distance class
 Compute the structure with maximum expected accuracy (MEA)
 Compute the centroid structure
 RNA-RNA interactionPredict structures formed by two molecules upon hybridization
 MFE Structures of two hybridized SequencesMFE 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 SequencesPartition Function Cofolding
 Partition Function for two hybridized Sequences as a stepwise ProcessRNA-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 predictionCompute 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 SpaceCompute Thermodynamic properties for a Distance Class Partitioning of the Secondary Structure Space
 Calculating MFE representatives of a Distance Based PartitioningCompute 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 PartitioningCompute 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 PartitioningContains 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 structuresHeuristics to explore direct, optimal (re-)folding paths between two secondary structures
 Experimental structure probing dataInclude experimental structure probing data to guide structure predictions
 SHAPE reactivity dataIncorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints
 Generate soft constraints from dataFind 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 structuresSimple extensions to model ligand binding to RNA structures
 Ligands binding to unstructured domainsAdd ligand binding to loop regions using the Unstructured domains feature
 Incorporating ligands binding to specific sequence/structure motifs using soft constraintsLigand binding to specific hairpin/interior loop like motifs using the Soft constraints feature
 Complex structured modules
 G-quadruplexesVarious functions related to G-quadruplex computations
 Data Structures and Preprocessor MacrosAll datastructures and typedefs shared among the Vienna RNA Package can be found here
 The Fold CompoundThis 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 MatricesThis 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 AlignmentsFunctions 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