RNAlib-2.5.1
Secondary Structure Utilities

Functions to create, parse, convert, manipulate, and compare secondary structure representations. More...

Detailed Description

Functions to create, parse, convert, manipulate, and compare secondary structure representations.

+ Collaboration diagram for Secondary Structure Utilities:

Modules

 Dot-Bracket Notation of Secondary Structures
 The Dot-Bracket notation as introduced already in the early times of the ViennaRNA Package denotes base pairs by matching pairs of parenthesis () and unpaired nucleotides by dots ..
 
 Washington University Secondary Structure (WUSS) notation
 The WUSS notation, as frequently used for consensus secondary structures in Stockholm 1.0 format.
 
 Pair Table Representation of Secondary Structures
 
 Pair List Representation of Secondary Structures
 
 Abstract Shapes Representation of Secondary Structures
 Abstract Shapes, introduced by Giegerich et al. in (2004) [10], collapse the secondary structure while retaining the nestedness of helices and hairpin loops.
 
 Helix List Representation of Secondary Structures
 
 Tree Representation of Secondary Structures
 Secondary structures can be readily represented as trees, where internal nodes represent base pairs, and leaves represent unpaired nucleotides. The dot-bracket structure string already is a tree represented by a string of parenthesis (base pairs) and dots for the leaf nodes (unpaired nucleotides).
 
 Distance measures between Secondary Structures
 
 Deprecated Interface for Secondary Structure Utilities
 

Files

file  structures.h
 Various utility- and helper-functions for secondary structure parsing, converting, etc.
 

Functions

int * vrna_loopidx_from_ptable (const short *pt)
 Get a loop index representation of a structure.
 
unsigned int * vrna_refBPcnt_matrix (const short *reference_pt, unsigned int turn)
 Make a reference base pair count matrix. More...
 
unsigned int * vrna_refBPdist_matrix (const short *pt1, const short *pt2, unsigned int turn)
 Make a reference base pair distance matrix. More...
 
char * vrna_db_from_probs (const FLT_OR_DBL *pr, unsigned int length)
 Create a dot-bracket like structure string from base pair probability matrix. More...
 
char vrna_bpp_symbol (const float *x)
 Get a pseudo dot bracket notation for a given probability information.
 
char * vrna_db_from_bp_stack (vrna_bp_stack_t *bp, unsigned int length)
 Create a dot-backet/parenthesis structure from backtracking stack. More...
 

Function Documentation

◆ vrna_refBPcnt_matrix()

unsigned int * vrna_refBPcnt_matrix ( const short *  reference_pt,
unsigned int  turn 
)

#include <ViennaRNA/utils/structures.h>

Make a reference base pair count matrix.

Get an upper triangular matrix containing the number of basepairs of a reference structure for each interval [i,j] with i<j. Access it via iindx!!!

◆ vrna_refBPdist_matrix()

unsigned int * vrna_refBPdist_matrix ( const short *  pt1,
const short *  pt2,
unsigned int  turn 
)

#include <ViennaRNA/utils/structures.h>

Make a reference base pair distance matrix.

Get an upper triangular matrix containing the base pair distance of two reference structures for each interval [i,j] with i<j. Access it via iindx!!!

◆ vrna_db_from_probs()

char * vrna_db_from_probs ( const FLT_OR_DBL pr,
unsigned int  length 
)

#include <ViennaRNA/utils/structures.h>

Create a dot-bracket like structure string from base pair probability matrix.

SWIG Wrapper Notes:
This function is available as parameter-less method db_from_probs() bound to objects of type fold_compound. Parameters pr and length are implicitely taken from the fold_compound object the method is bound to. Upon missing base pair probabilities, this method returns an empty string.

◆ vrna_db_from_bp_stack()

char * vrna_db_from_bp_stack ( vrna_bp_stack_t bp,
unsigned int  length 
)

#include <ViennaRNA/utils/structures.h>

Create a dot-backet/parenthesis structure from backtracking stack.

This function is capable to create dot-bracket structures from suboptimal structure prediction sensu M. Zuker

Parameters
bpBase pair stack containing the traced base pairs
lengthThe length of the structure
Returns
The secondary structure in dot-bracket notation as provided in the input