RNAlib 2.4.6
  • Index
      • Getting Started
        • Installation and Configuration
          • Installing the ViennaRNA Package
          • Quick-start
          • Installation without root privileges
          • Notes for MacOS X users
          • Configuring RNAlib features
          • Streaming SIMD Extension (SSE) support
          • Scripting Interfaces
          • Cluster Analysis
          • Kinfold
          • RNAforester
          • Kinwalker
          • Link Time Optimization (LTO)
          • OpenMP support
          • POSIX threads (pthread) support
          • Stochastic backtracking using Boustrophedon scheme
          • SVM Z-score filter in RNALfold
          • GNU Scientific Library
          • Disable C11/C++11 feature support
          • Enable warnings for use of deprecated symbols
          • Single precision partition function
          • Help
          • Linking against RNAlib
          • Compiler and Linker flags
          • The pkg-config tool
        • HelloWorld
        • HelloWorld (Perl/Python)
          • Perl5
          • Python
      • Concepts and Algorithms
        • RNA Structure
          • RNA Structures
          • Levels of Structure Abstraction
          • Primary Structure
          • Secondary Structure
          • Tertiary Structure
          • Quarternary Structure
          • Pseudo-Knots
        • Distance Measures
          • Functions for Tree Edit Distances
          • Functions for String Alignment
          • Functions for Comparison of Base Pair Probabilities
        • Free Energy of Secondary Structures
          • Secondary Structure Loop Decomposition
          • Free Energy Evaluation API
          • Free Energy Parameters
          • Free Energy Parameters Modification API
          • Fine-tuning of the Energy Evaluation Model
        • Secondary Structure Folding Grammar
          • Secondary Structure Folding Recurrences
          • Additional Structural Domains
          • Structured Domains
          • Unstructured Domains
          • Domain Extension API
          • Constraints on the Folding Grammar
          • Hard Constraints API
          • Soft Constraints API
        • RNA Secondary Structure Landscapes
          • The Neighborhood of a Secondary Structure
          • The Secondary Structure Landscape API
        • Minimum Free Energy Algorithm(s)
          • Zuker’s Algorithm
          • MFE for circular RNAs
          • MFE Algorithm API
        • Partition Function and Equilibrium Probabilitiy Algorithm(s)
          • Equilibrium Ensemble Statistics
          • Partition Function and Equilibrium Probability API
        • Suboptimals and (other) Representative Structures
          • Suboptimal Secondary Structures
          • Sampling Secondary Structures from the Ensemble
          • Structure Enumeration and Sampling API
        • RNA-RNA Interaction
          • rip_intro
          • rip_intro
          • RNA-RNA interaction as a Stepwise Process
          • RNA-RNA Interaction API
        • Locally Stable Secondary Structures
          • local_intro
          • local_mfe
          • local_pf
          • Locally Stable Secondary Structure API
        • Comparative Structure Prediction
          • Incorporate Evolutionary Information
          • Comparative Structure Prediction API
        • Classified DP variations
          • The Idea of Classified Dynamic Programming
          • Distance Class Partitioning
          • Density of States (DOS)
          • Classified DP API
        • RNA Sequence Design
          • Generate Sequences that fold into particular Secondary Structures
          • RNA Sequence Design API
        • Experimental Structure Probing Data
          • Guide the Structure Prediction using Experimental Data
          • SHAPE reactivities
          • Structure Probing Data API
        • Ligand Binding
          • Small Molecules and Proteins that bind to specific RNA Structures
          • ligand_binding_api
        • (Tertiary) Structure Motifs
          • Incorporating Higher-Order (Tertiary) Structure Motifs
          • RNA G-Quadruplexes
          • (Tertiary) Structure Motif API
      • I/O Formats
        • RNA Structure Notations
          • Representations of Secondary Structures
          • Dot-Bracket Notation (a.k.a. Dot-Parenthesis Notation)
          • Extended Dot-Bracket Notation
          • Washington University Secondary Structure (WUSS) notation
          • Examples for Structure Parsing and Conversion
          • Structure Parsing and Conversion API
        • File Formats
          • File formats for Multiple Sequence Alignments (MSA)
          • ClustalW format
          • Stockholm 1.0 format
          • FASTA (Pearson) format
          • MAF format
          • File formats to manipulate the RNA folding grammar
          • Command Files
          • Constraint commands
          • RNA folding grammar exensions
          • Specification of the loop type context
          • Controlling the orientation of base pairing
          • Sequence coordinates
          • Valid constraint commands
          • Valid domain extensions commands
        • Plotting
          • Producing secondary structure graphs
          • Producing (colored) dot plots for base pair probabilities
          • Producing (colored) alignments
      • Basic Data Structures
        • Sequence and Structure Data
        • The ‘Fold Compound’
        • Model Details
      • API Features
        • RNAlib API v3.0
          • Introduction
          • What are the major changes?
          • How to port your program to the new API
          • Some Examples using RNAlib API v3.0
        • Callback Functions
          • The purpose of Callback mechanisms
          • List of available Callbacks
        • Scripting Language interface(s)
          • Introduction
          • Function renaming scheme
          • Object oriented Interface for data structures
          • Examples
          • SWIG generated Wrapper notes
      • Additional Utilities
      • Examples
        • C Examples
          • Hello World Examples
          • First Steps with the Fold Compound
          • Writing Callback Functions
          • Application of Soft Constraints
          • Other Examples
          • Deprecated Examples
        • Perl5 Examples
        • Python Examples
      • Changelog
      • Deprecated List
      • Bug List
      • Bibliography
      • The RNAlib API
        • Data Structures and Preprocessor Macros
          • The Dynamic Programming Matrices
            • enum vrna_mx_type_e
              • Overview
              • Detailed Documentation
                • Enum Values
            • struct vrna_mx_mfe_s
              • Overview
              • Detailed Documentation
              • Fields
            • struct vrna_mx_pf_s
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
          • The Fold Compound
            • enum vrna_fc_type_e
              • Overview
              • Detailed Documentation
                • Enum Values
            • struct vrna_fc_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
            • Macros
          • struct constrain
          • struct dupVar
          • struct duplexT
          • struct interact
            • Overview
            • Detailed Documentation
            • Fields
          • struct node
          • struct pu_contrib
            • Overview
            • Detailed Documentation
            • Fields
          • struct pu_out
            • Overview
            • Detailed Documentation
            • Fields
          • struct snoopT
          • struct vrna_basepair_s
          • struct vrna_bp_stack_s
          • struct vrna_color_s
          • struct vrna_cpair_s
          • struct vrna_data_linear_s
          • struct vrna_sect_s
          • Overview
          • Detailed Documentation
          • Typedefs
          • Global Functions
        • Utilities
          • Utilities for sequence alignments
            • struct vrna_pinfo_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
            • Macros
          • Functions that provide dynamically buffered stream-like data structures
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
          • Functions to Read/Write several File Formats for RNA Sequences, Structures, and Alignments
            • enum vrna_command_e
            • struct vrna_command_s
              • Overview
              • Detailed Documentation
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
            • Macros
          • Functions for Creating Secondary Structure Plots, Dot-Plots, and More
            • Functions to generate annotations for Secondary Structure Plots, Dot-Plots, and Others
              • Overview
              • Detailed Documentation
              • Global Functions
            • struct COORDINATE
            • struct vrna_dotplot_auxdata_t
            • Overview
            • Detailed Documentation
            • Global Variables
            • Global Functions
            • Macros
          • Parsing, converting, and comparing sequences
            • Overview
            • Detailed Documentation
            • Global Functions
            • Macros
          • Parsing, converting, comparing secondary structures
            • struct vrna_elem_prob_s
              • Overview
              • Detailed Documentation
            • struct vrna_hx_s
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Variables
            • Global Functions
            • Macros
          • Functions to convert between various units
            • enum vrna_unit_energy_e
              • Overview
              • Detailed Documentation
                • Enum Values
            • enum vrna_unit_temperature_e
              • Overview
              • Detailed Documentation
                • Enum Values
            • Overview
            • Detailed Documentation
            • Global Functions
          • Overview
          • Detailed Documentation
          • Global Variables
          • Global Functions
          • Macros
        • Classified Dynamic Programming variants
          • Compute the Density of States
            • Overview
            • Detailed Documentation
            • Global Variables
          • Distance based partitioning of the Secondary Structure Space
            • Calculating MFE representatives of a Distance Based Partitioning
              • struct TwoDfold_vars
                • Overview
                • Detailed Documentation
                • Fields
              • struct vrna_sol_TwoD_t
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
            • Calculate Partition Functions of a Distance Based Partitioning
              • struct vrna_sol_TwoD_pf_t
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
            • Stochastic Backtracking of Structures from Distance Based Partitioning
              • Overview
              • Detailed Documentation
              • Global Functions
        • RNA-RNA interaction
          • MFE Structures of two hybridized Sequences
            • Overview
            • Detailed Documentation
            • Global Functions
          • Partition Function for two hybridized Sequences
            • struct vrna_dimer_pf_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Variables
            • Global Functions
          • Partition Function for two hybridized Sequences as a stepwise Process
            • Overview
            • Detailed Documentation
            • Global Functions
        • The RNA folding grammar
          • Constraining the RNA folding grammar
            • Hard constraints
              • struct vrna_hc_s
                • Overview
                • Detailed Documentation
                • Fields
              • struct vrna_hc_up_s
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
              • Macros
            • Soft constraints
              • struct vrna_sc_s
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
            • Overview
            • Detailed Documentation
            • Global Functions
            • Macros
          • Extending the folding grammar with additional domains
            • Unstructured domains
              • struct vrna_unstructured_domain_s
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
              • Macros
          • Energy parameters
            • Reading/Writing Energy Parameter Sets from/to File
              • Converting Energy Parameter Files
                • Overview
                • Detailed Documentation
                • Global Functions
                • Macros
              • enum parset
              • Overview
              • Detailed Documentation
              • Global Functions
            • struct vrna_exp_param_s
              • Overview
              • Detailed Documentation
              • Fields
            • struct vrna_param_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
          • Fine-tuning of the implemented models
            • struct vrna_md_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Variables
            • Global Functions
            • Macros
          • struct vrna_gr_aux_s
        • The RNA secondary structure landscape
          • Neighborhood relation and move sets for secondary structures
            • struct vrna_move_s
              • Overview
              • Detailed Documentation
              • Fields
            • Overview
            • Detailed Documentation
            • Global Functions
            • Macros
          • Refolding paths of secondary structures
            • Direct refolding paths between two secondary structures
              • struct vrna_path_s
                • Overview
                • Detailed Documentation
                • Fields
              • Overview
              • Detailed Documentation
              • Typedefs
              • Global Functions
            • Overview
            • Detailed Documentation
            • Global Functions
            • Macros
        • Comparative structure prediction
          • MFE Consensus Structures for Sequence Alignment(s)
            • Overview
            • Detailed Documentation
            • Global Functions
          • Partition Function and Base Pair Probabilities for Sequence Alignment(s)
            • Overview
            • Detailed Documentation
            • Global Functions
          • Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)
            • Overview
            • Detailed Documentation
            • Global Functions
          • Local MFE Consensus Structure Prediction for Sequence Alignments
            • Overview
            • Detailed Documentation
            • Global Functions
          • Overview
          • Detailed Documentation
          • Global Variables
          • Global Functions
        • Suboptimals and representative structures
          • Compute the centroid structure
            • Overview
            • Detailed Documentation
            • Global Functions
          • Compute the structure with maximum expected accuracy (MEA)
            • Overview
            • Detailed Documentation
            • Global Functions
          • Structure sampling from the ensemble
            • Overview
            • Detailed Documentation
            • Global Variables
            • Global Functions
          • Suboptimal structures within an energy band arround the MFE
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Variables
            • Global Functions
          • Suboptimal structures sensu Stiegler et al. 1984 / Zuker et al. 1989
            • Overview
            • Detailed Documentation
            • Global Functions
        • Ligands binding to RNA structures
          • Incorporating ligands binding to specific sequence/structure motifs using soft constraints
            • Overview
            • Detailed Documentation
            • Global Functions
        • Experimental structure probing data
          • SHAPE reactivity data
            • Overview
            • Detailed Documentation
            • Global Functions
          • Generate soft constraints from data
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
            • Macros
        • Partition function and equilibrium properties
          • Overview
          • Detailed Documentation
          • Global Functions
        • Free energy evaluation
          • Process and evaluate individual loops
            • Overview
            • Detailed Documentation
            • Typedefs
            • Global Functions
          • Overview
          • Detailed Documentation
          • Global Variables
          • Global Functions
        • Minimum Free Energy (MFE) algorithms
          • MFE Structures of single Nucleic Acid Sequences
            • Overview
            • Detailed Documentation
            • Global Functions
          • Overview
          • Detailed Documentation
          • Typedefs
          • Global Functions
        • Complex structured modules
          • G-quadruplexes
            • Overview
            • Detailed Documentation
            • Global Functions
        • Inverse Folding (Design)
          • Overview
          • Detailed Documentation
          • Global Variables
          • Global Functions
        • Locally stable structures
          • Local MFE Structure Prediction and Z-scores
            • Overview
            • Detailed Documentation
            • Global Functions
          • Partition Function and Equilibrium Probabilities for Locally Stable Secondary Structures
            • Overview
            • Detailed Documentation
            • Global Functions
            • Macros
        • Global Namespace
          • enum MOVE_TYPE
          • enum vrna_hc_type_e
            • Overview
            • Detailed Documentation
              • Enum Values
          • enum vrna_sc_type_e
            • Overview
            • Detailed Documentation
              • Enum Values
          • enum vrna_seq_type_e
            • Overview
            • Detailed Documentation
              • Enum Values
          • struct Postorder_list
          • struct Tree
          • struct TwoDpfold_vars
            • Overview
            • Detailed Documentation
            • Fields
          • struct _struct_en
          • struct swString
          • struct vrna_dimer_conc_s
            • Overview
            • Detailed Documentation
            • Fields
          • struct vrna_hc_bp_storage_t
          • struct vrna_sc_bp_storage_t
          • struct vrna_sc_motif_s
          • struct vrna_sequence_s
            • Overview
            • Detailed Documentation
            • Fields
          • struct vrna_structured_domains_s
          • struct vrna_subopt_sol_s
            • Overview
            • Detailed Documentation
            • Fields
          • struct vrna_unstructured_domain_motif_s
          • Overview
          • Detailed Documentation
          • Typedefs
          • Global Variables
          • Global Functions
          • Macros
  • Page
      • Getting Started
      • Concepts and Algorithms
      • I/O Formats
      • Basic Data Structures
      • API Features
      • Additional Utilities
      • Examples
      • Changelog
      • Deprecated List
      • Bug List
      • Bibliography
      • The RNAlib API
        • Data Structures and Preprocessor Macros
        • Utilities
        • Classified Dynamic Programming variants
        • RNA-RNA interaction
        • The RNA folding grammar
        • The RNA secondary structure landscape
        • Comparative structure prediction
        • Suboptimals and representative structures
          • Compute the centroid structure
          • Compute the structure with maximum expected accuracy (MEA)
          • Structure sampling from the ensemble
          • Suboptimal structures within an energy band arround the MFE
          • Suboptimal structures sensu Stiegler et al. 1984 / Zuker et al. 1989
        • Ligands binding to RNA structures
        • Experimental structure probing data
        • Partition function and equilibrium properties
        • Free energy evaluation
        • Minimum Free Energy (MFE) algorithms
        • Complex structured modules
        • Inverse Folding (Design)
        • Locally stable structures
        • Global Namespace
  • « Local MFE Con...
  • Compute the c... »
  • Getting Started
  • Concepts and Algorithms
  • I/O Formats
  • Basic Data Structures
  • API Features
  • Additional Utilities
  • Examples
  • Changelog
  • Deprecated List
  • Bug List
  • Bibliography
  • The RNAlib API
    • Data Structures and Preprocessor Macros
    • Utilities
    • Classified Dynamic Programming variants
    • RNA-RNA interaction
    • The RNA folding grammar
    • The RNA secondary structure landscape
    • Comparative structure prediction
    • Suboptimals and representative structures
      • Compute the centroid structure
      • Compute the structure with maximum expected accuracy (MEA)
      • Structure sampling from the ensemble
      • Suboptimal structures within an energy band arround the MFE
      • Suboptimal structures sensu Stiegler et al. 1984 / Zuker et al. 1989
    • Ligands binding to RNA structures
    • Experimental structure probing data
    • Partition function and equilibrium properties
    • Free energy evaluation
    • Minimum Free Energy (MFE) algorithms
    • Complex structured modules
    • Inverse Folding (Design)
    • Locally stable structures
    • Global Namespace

Suboptimals and representative structures¶

Sample and enumerate suboptimal secondary structures from RNA sequence data.
Compute the centroid structure
Compute the structure with maximum expected accuracy (MEA)
Structure sampling from the ensemble
Suboptimal structures within an energy band arround the MFE
Suboptimal structures sensu Stiegler et al. 1984 / Zuker et al. 1989

Back to top

© Copyright 2017, Ronny Lorenz.
Created using Sphinx 1.7.3.