G-Quadruplexes

Introduction

Energy Evaluation

Functions

int vrna_E_gquad(unsigned int L, unsigned int l[3], vrna_param_t *P)
#include <ViennaRNA/eval/gquad.h>
FLT_OR_DBL vrna_exp_E_gquad(unsigned int L, unsigned int l[3], vrna_exp_param_t *pf)
#include <ViennaRNA/eval/gquad.h>
void vrna_E_consensus_gquad(unsigned int L, unsigned int l[3], unsigned int position, unsigned int length, unsigned int n_seq, const short **S, const unsigned int **a2s, vrna_param_t *P, int en[2])
#include <ViennaRNA/eval/gquad.h>
FLT_OR_DBL vrna_exp_E_consensus_gquad(unsigned int L, unsigned int l[3], vrna_exp_param_t *pf, unsigned int position, unsigned int length, unsigned int n_seq, const short **S, const unsigned int **a2s)
#include <ViennaRNA/eval/gquad.h>
int vrna_mfe_gquad_internal_loop(vrna_fold_compound_t *fc, unsigned int i, unsigned int j)
#include <ViennaRNA/mfe/gquad.h>
FLT_OR_DBL vrna_gq_int_loop_pf(vrna_fold_compound_t *fc, unsigned int i, unsigned int j)
#include <ViennaRNA/partfunc/gquad.h>
vrna_array (int) vrna_gq_int_loop_subopt(vrna_fold_compound_t *fc
#include <ViennaRNA/subopt/gquad.h>
unsigned int unsigned int vrna_array (unsigned int) *p_p
#include <ViennaRNA/subopt/gquad.h>
void get_gquad_pattern_exhaustive(short *S, unsigned int i, unsigned int j, vrna_param_t *P, unsigned int *L, unsigned int *l, int threshold)
#include <ViennaRNA/subopt/gquad.h>
unsigned int get_gquad_count(short *S, unsigned int i, unsigned int j)
#include <ViennaRNA/subopt/gquad.h>

Variables

unsigned int i
unsigned int unsigned int j
unsigned int unsigned int int threshold

Dynamic Programming Matrices

Functions

vrna_smx_csr_FLT_OR_DBL_t *vrna_gq_pos_pf(vrna_fold_compound_t *fc)
#include <ViennaRNA/partfunc/gquad.h>

Backtracking

Functions

int vrna_bt_gquad(vrna_fold_compound_t *fc, unsigned int i, unsigned int j, unsigned int *L, unsigned int l[3])
#include <ViennaRNA/backtrack/gquad.h>
int vrna_bt_gquad_mfe(vrna_fold_compound_t *fc, unsigned int i, unsigned int j, vrna_bps_t bp_stack)
#include <ViennaRNA/backtrack/gquad.h>
int vrna_bt_gquad_internal(vrna_fold_compound_t *fc, unsigned int i, unsigned int j, int en, vrna_bps_t bp_stack, vrna_bts_t bt_stack)
#include <ViennaRNA/backtrack/gquad.h>

Parsing

Functions

void get_gquad_pattern_pf(short *S, int i, int j, vrna_exp_param_t *pf, int *L, int l[3])
#include <ViennaRNA/partfunc/gquad.h>
void vrna_get_gquad_pattern_pf(vrna_fold_compound_t *fc, unsigned int i, unsigned int j, unsigned int *L, unsigned int[3])
#include <ViennaRNA/partfunc/gquad.h>
unsigned int vrna_gq_parse(const char *db_string, unsigned int *L, unsigned int l[3])
#include <ViennaRNA/structures/dotbracket.h>

Parse a G-Quadruplex from a dot-bracket structure string.

Given a dot-bracket structure (possibly) containing gquads encoded by ‘+’ signs (and an optional ‘~’ end sign, find first gquad, return end position (1-based) or 0 if none found. Upon return L and l[] contain the number of stacked layers, as well as the lengths of the linker regions.

To parse a string with many gquads, call vrna_gq_parse() repeatedly e.g.

end1 = vrna_gq_parse(struc, &L, l); ... ;
end2 = vrna_gq_parse(struc+end1, &L, l); end2+=end1; ... ;
end3 = vrna_gq_parse(struc+end2, &L, l); end3+=end2; ... ;

Note

For circular RNAs and G-Quadruplexes spanning the n,1-junction the sum of linkers and g-runs is lower than the end position. This condition can be used to check whether or not to accept a G-Quadruplex parsed from the dot-bracket string. Also note, that such n,1-junction spanning G-Quadruplexes must end with a ~ sign, to be unambigous.

Parameters:

  • db_string – The input structure in dot-bracket notation

  • L – A pointer to an unsigned integer to store the layer (stack) size

  • l – An array of three values to store the respective linker lenghts

Returns:

The end position of the G-Quadruplex (1-based) or 0 if not found

void vrna_db_insert_gq(char *db, unsigned int i, unsigned int L, unsigned int l[3], unsigned int n)
#include <ViennaRNA/structures/dotbracket.h>
plist *get_plist_gquad_from_db(const char *structure, float pr)
#include <ViennaRNA/structures/problist.h>

Other

Functions

plist * get_plist_gquad_from_pr (short *S, int gi, int gj, vrna_smx_csr(FLT_OR_DBL) *q_gq, FLT_OR_DBL *probs, FLT_OR_DBL *scale, vrna_exp_param_t *pf)
#include <ViennaRNA/partfunc/gquad.h>
vrna_ep_t *vrna_plist_gquad_from_pr(vrna_fold_compound_t *fc, int gi, int gj)
#include <ViennaRNA/partfunc/gquad.h>
plist * get_plist_gquad_from_pr_max (short *S, int gi, int gj, vrna_smx_csr(FLT_OR_DBL) *q_gq, FLT_OR_DBL *probs, FLT_OR_DBL *scale, int *L, int l[3], vrna_exp_param_t *pf)
#include <ViennaRNA/partfunc/gquad.h>
vrna_ep_t *vrna_plist_gquad_from_pr_max(vrna_fold_compound_t *fc, unsigned int gi, unsigned int gj, unsigned int *Lmax, unsigned int lmax[3])
#include <ViennaRNA/partfunc/gquad.h>

Deprecated

Functions

int vrna_BT_gquad_mfe(vrna_fold_compound_t *fc, int i, int j, vrna_bp_stack_t *bp_stack, unsigned int *stack_count)
#include <ViennaRNA/backtrack/gquad.h>
int vrna_BT_gquad_int(vrna_fold_compound_t *fc, int i, int j, int en, vrna_bp_stack_t *bp_stack, unsigned int *stack_count)
#include <ViennaRNA/backtrack/gquad.h>
int backtrack_GQuad_IntLoop_L(int c, int i, int j, int type, short *S, int **ggg, int maxdist, int *p, int *q, vrna_param_t *P)
#include <ViennaRNA/backtrack/gquad.h>

backtrack an internal loop like enclosed g-quadruplex with closing pair (i,j) with underlying Lfold matrix

Parameters:

  • c – The total contribution the loop should resemble

  • i – position i of enclosing pair

  • j – position j of enclosing pair

  • type – base pair type of enclosing pair (must be reverse type)

  • S – integer encoded sequence

  • ggg – triangular matrix containing g-quadruplex contributions

  • p – here the 5’ position of the gquad is stored

  • q – here the 3’ position of the gquad is stored

  • P – the datastructure containing the precalculated contibutions

Returns:

1 on success, 0 if no gquad found

int backtrack_GQuad_IntLoop_L_comparative(int c, int i, int j, unsigned int *type, short *S_cons, short **S5, short **S3, unsigned int **a2s, int **ggg, int *p, int *q, int n_seq, vrna_param_t *P)
#include <ViennaRNA/backtrack/gquad.h>
int E_gquad(int L, int l[3], vrna_param_t *P)
#include <ViennaRNA/eval/gquad.h>
FLT_OR_DBL exp_E_gquad(int L, int l[3], vrna_exp_param_t *pf)
#include <ViennaRNA/eval/gquad.h>
void E_gquad_ali_en(int i, int L, int l[3], const short **S, unsigned int **a2s, unsigned int n_seq, vrna_param_t *P, int en[2])
#include <ViennaRNA/eval/gquad.h>
FLT_OR_DBL exp_E_gquad_ali(int i, int L, int l[3], short **S, unsigned int **a2s, int n_seq, vrna_exp_param_t *pf)
#include <ViennaRNA/eval/gquad.h>
DEPRECATED (FLT_OR_DBL *get_gquad_pf_matrix(short *S, FLT_OR_DBL *scale, vrna_exp_param_t *pf), "Use vrna_gq_pos_pf() instead")
#include <ViennaRNA/partfunc/gquad.h>
DEPRECATED (FLT_OR_DBL *get_gquad_pf_matrix_comparative(unsigned int n, short *S_cons, short **S, unsigned int **a2s, FLT_OR_DBL *scale, unsigned int n_seq, vrna_exp_param_t *pf), "Use vrna_gq_pos_pf() instead")
#include <ViennaRNA/partfunc/gquad.h>
int parse_gquad(const char *struc, int *L, int l[3])
#include <ViennaRNA/structures/dotbracket.h>

Parse a G-Quadruplex from a dot-bracket structure string.

Given a dot-bracket structure (possibly) containing gquads encoded by ‘+’ signs, find first gquad, return end position or 0 if none found Upon return L and l[] contain the number of stacked layers, as well as the lengths of the linker regions. To parse a string with many gquads, call parse_gquad repeatedly e.g. end1 = parse_gquad(struc, &L, l); … ; end2 = parse_gquad(struc+end1, &L, l); end2+=end1; … ; end3 = parse_gquad(struc+end2, &L, l); end3+=end2; … ;