Functions to create, parse, convert, manipulate, and compare secondary structure representations. More...
Functions to create, parse, convert, manipulate, and compare secondary structure representations.
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... | |
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!!!
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!!!
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.
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. 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
bp | Base pair stack containing the traced base pairs |
length | The length of the structure |