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RNAlib-2.5.0
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Functions to create, parse, convert, manipulate, and compare secondary structure representations. More...
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... | |
| 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 |