seq_align.h File Reference

Header file for functions to generate and analyze dot plots. More...

#include "rwmolecule.h"
#include "rwresprop.h"
#include "Matrix.h"

Functions
long	seq_pair_align (Bmolecule *mol1, Bmolecule *mol2, double gapopen, double gapextend, Bresidue_matrix *simat)
	Aligns two sequences. More...
int	seq_find_best_offset (Bmolecule *mol1, Bmolecule *mol2, long &nres, Bresidue_matrix *simat)
	Finds the best offset for aligning two sequences without gaps. More...
Matrix	seq_dot_plot (Bmolecule *mol1, Bmolecule *mol2, Bresidue_matrix *simat)
	Calculates a dot plot for two sequences. More...
Matrix	seq_dot_plot_mov_avg (Matrix dot_plot, int window)
	Calculates a moving average along the diagonals of a dot plot. More...
int	seq_dot_plot_interpret (Matrix dot_plot)
	Finds the row and column maxima in a dot plot. More...
double	seq_dot_plot_best_segments (Matrix dot_plot)
	Finding the best segments in a dot plot. More...
int	seq_show_segments (Bmolecule *mol1, Bmolecule *mol2, double threshold, Matrix dot_plot)
	Finds the best offset for aligning two sequences without gaps. More...

Detailed Description

Header file for functions to generate and analyze dot plots.

Author

Bernard Heymann

Date

Created: 20001029

Modified: 20110411

Function Documentation

seq_dot_plot()

Matrix seq_dot_plot	(	Bmolecule *	mol1,
		Bmolecule *	mol2,
		Bresidue_matrix *	simat
	)

Calculates a dot plot for two sequences.

Parameters

*mol1	first molecule structure.
*mol2	second molecule structure.
*simat	residue similarity matrix.

Returns

Matrix matrix with dot plot.

seq_dot_plot_best_segments()

double seq_dot_plot_best_segments

(

Matrix

dot_plot

)

Finding the best segments in a dot plot.

Parameters

dot_plot

dot plot matrix.

Returns

double threshold to identify unique segments.

seq_dot_plot_interpret()

int seq_dot_plot_interpret

(

Matrix

dot_plot

)

Finds the row and column maxima in a dot plot.

Parameters

dot_plot

dot plot matrix.

Returns

int number of maxima in both rows and columns.

seq_dot_plot_mov_avg()

Matrix seq_dot_plot_mov_avg	(	Matrix	dot_plot,
		int	window
	)

Calculates a moving average along the diagonals of a dot plot.

Parameters

dot_plot	dot plot matrix.
window	moving average window size.

Returns

Matrix matrix with moving average dot plot.

seq_find_best_offset()

int seq_find_best_offset	(	Bmolecule *	mol1,
		Bmolecule *	mol2,
		long &	nres,
		Bresidue_matrix *	simat
	)

Finds the best offset for aligning two sequences without gaps.

Parameters

*mol1	first molecule structure.
*mol2	second molecule structure.
*nres	number of similar residues in best diagonal.
*simat	residue similarity matrix.

Returns

int the offset of sequence 2 with respect to sequence 1.

The best offset is determined as the diagonal of a dot plot with
the highest value.

seq_pair_align()

long seq_pair_align	(	Bmolecule *	mol1,
		Bmolecule *	mol2,
		double	gapopen,
		double	gapextend,
		Bresidue_matrix *	simat
	)

Aligns two sequences.

Parameters

*mol1	first molecule structure.
*mol2	second molecule structure.
gapopen	gap opening penalty.
gapextend	gap extension penalty.
*simat	residue similarity matrix.

Returns

long length of the aligned sequences.

Two sequences are aligned and returned in the sequence strings
of the molecule structures.

seq_show_segments()

int seq_show_segments	(	Bmolecule *	mol1,
		Bmolecule *	mol2,
		double	threshold,
		Matrix	dot_plot
	)

Finds the best offset for aligning two sequences without gaps.

Parameters

*mol1	first molecule structure.
*mol2	second molecule structure.
threshold	threshold to identify segments.
dot_plot	dot plot.

Returns

int the offset of sequence 2 with respect to sequence 1.

The best offset is determined as the diagonal of a dot plot with
the highest value.