gquad.h File Reference

Various functions related to G-quadruplex computations. More...

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Functions
int *	get_gquad_matrix (short *S, paramT *P)
	Get a triangular matrix prefilled with minimum free energy contributions of G-quadruplexes. More...
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, paramT *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, paramT *P)

Detailed Description

Various functions related to G-quadruplex computations.

Function Documentation

int* get_gquad_matrix	(	short *	S,
		paramT *	P
	)

Get a triangular matrix prefilled with minimum free energy contributions of G-quadruplexes.

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().

See Also

get_jindx(), encode_sequence()

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

int parse_gquad	(	const char *	struc,
		int *	L,
		int	l[3]
	)

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; ... ;

PRIVATE int backtrack_GQuad_IntLoop	(	int	c,
		int	i,
		int	j,
		int	type,
		short *	S,
		int *	ggg,
		int *	index,
		int *	p,
		int *	q,
		paramT *	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,
		paramT *	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