Various functions related to G-quadruplex computations. More…
// global functions int E_gquad ( int L, int l [3], vrna_param_t* P ) FLT_OR_DBL exp_E_gquad ( int L, int l [3], vrna_exp_param_t* pf ) int E_gquad_ali ( int i, int L, int l [3], const short** S, int n_seq, vrna_param_t* P ) void E_gquad_ali_en ( int i, int L, int l [3], const short** S, int n_seq, int en [2], vrna_param_t* P ) int* get_gquad_matrix ( short* S, vrna_param_t* P ) int* get_gquad_ali_matrix ( short* S_cons, short** S, int n_seq, vrna_param_t* P ) FLT_OR_DBL* get_gquad_pf_matrix ( short* S, FLT_OR_DBL* scale, vrna_exp_param_t* pf ) int** get_gquad_L_matrix ( short* S, int start, int maxdist, int n, int** g, vrna_param_t* P ) void vrna_gquad_mx_local_update ( vrna_fold_compound_t* vc, int start ) void get_gquad_pattern_mfe ( short* S, int i, int j, vrna_param_t* P, int* L, int l [3] ) void get_gquad_pattern_exhaustive ( short* S, int i, int j, vrna_param_t* P, int* L, int* l, int threshold ) void get_gquad_pattern_pf ( short* S, int i, int j, vrna_exp_param_t* pf, int* L, int l [3] ) plist* get_plist_gquad_from_pr ( short* S, int gi, int gj, FLT_OR_DBL* G, FLT_OR_DBL* probs, FLT_OR_DBL* scale, vrna_exp_param_t* pf ) plist* get_plist_gquad_from_pr_max ( short* S, int gi, int gj, FLT_OR_DBL* G, FLT_OR_DBL* probs, FLT_OR_DBL* scale, int* L, int l [3], vrna_exp_param_t* pf ) plist* get_plist_gquad_from_db ( const char* structure, float pr ) int get_gquad_count ( short* S, int i, int j ) int get_gquad_layer_count ( short* S, int i, int j ) void get_gquad_pattern_mfe_ali ( short** S, short* S_cons, int n_seq, int i, int j, vrna_param_t* P, int* L, int l [3] ) int parse_gquad ( const char* struc, int* L, int l [3] ) PRIVATE int backtrack_GQuad_IntLoop ( int c, int i, int j, int type, short* S, int* ggg, int* index, int* p, int* q, vrna_param_t* P ) PRIVATE int backtrack_GQuad_IntLoop_comparative ( int c, int i, int j, unsigned int* type, short* S_cons, short** S5, short** S3, int* ggg, int* index, int* p, int* q, int n_seq, vrna_param_t* P ) PRIVATE 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 ) PRIVATE int vrna_BT_gquad_int ( vrna_fold_compound_t* vc, int i, int j, int en, vrna_bp_stack_t* bp_stack, int* stack_count ) PRIVATE int vrna_BT_gquad_mfe ( vrna_fold_compound_t* vc, int i, int j, vrna_bp_stack_t* bp_stack, int* stack_count ) PRIVATE int backtrack_GQuad_IntLoop_L_comparative ( int c, int i, int j, unsigned int* type, short* S_cons, short** S5, short** S3, int** ggg, int* p, int* q, int n_seq, vrna_param_t* P ) PRIVATE int E_GQuad_IntLoop ( int i, int j, int type, short* S, int* ggg, int* index, vrna_param_t* P ) PRIVATE int* E_GQuad_IntLoop_exhaustive ( int i, int j, int** p_p, int** q_p, int type, short* S, int* ggg, int threshold, int* index, vrna_param_t* P ) PRIVATE int E_GQuad_IntLoop_L ( int i, int j, int type, short* S, int** ggg, int maxdist, vrna_param_t* P ) PRIVATE FLT_OR_DBL exp_E_GQuad_IntLoop ( int i, int j, int type, short* S, FLT_OR_DBL* G, FLT_OR_DBL* scale, int* index, vrna_exp_param_t* pf )
int* get_gquad_matrix ( short* S, vrna_param_t* P )
At each position ij in the matrix, the minimum free energy of any G-quadruplex delimited by i and j is stored. If no G-quadruplex formation is possible, the matrix element is set to INF. Access the elements in the matrix via matrix[indx[j]+i]. To get the integer array indx see get_jindx().
Parameters:
S | The encoded sequence |
P | A pointer to the data structure containing the precomputed energy contributions |
Returns:
A pointer to the G-quadruplex contribution matrix
See also:
get_jindx(), encode_sequence()
int parse_gquad ( const char* struc, int* L, int l [3] )
PRIVATE int backtrack_GQuad_IntLoop ( int c, int i, int j, int type, short* S, int* ggg, int* index, int* p, int* q, vrna_param_t* P )
backtrack an interior loop like enclosed g-quadruplex with closing pair (i,j)
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 |
index | the index for accessing the triangular matrix |
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
PRIVATE 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 )
backtrack an interior 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