Hitmap 1.3
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Macros | Functions | Variables
SWseq.c File Reference
#include <hitmap.h>
#include "SWcommon.h"
#include "SWcommon_hit.h"
Include dependency graph for SWseq.c:

Go to the source code of this file.

Macros

#define h(i, j)   (hit_tileElemAtNoStride(H,2,i,j))
 
#define xback(i, j)   (hit_tileElemAtNoStride(xTraceback,2,i,j))
 
#define yback(i, j)   (hit_tileElemAtNoStride(yTraceback,2,i,j))
 

Functions

void phase_read_sequences ()
 
void phase_comp_hmatrix ()
 
void phase_comp_back ()
 
int main (int argc, char *argv[])
 

Variables

HitTile_aa_t p1
 
HitTile_aa_t p2
 
HitTile_h_t H
 
HitTile_trace_t xTraceback
 
HitTile_trace_t yTraceback
 
HitTile_aa_t out1
 
HitTile_aa_t out2
 
int xMax
 
int yMax
 
int xBegin
 
int yBegin
 
int match_length
 
int match_length1
 
int match_length2
 
int match_pos
 

Detailed Description

Hitmap Parallel version for the Smith-Waterman algorihtm. The Smith–Waterman algorithm performs local sequence alignment of protein sequences.

This version assumes a linear gap penalty. This algorithm creates the matrix H as follows:

              | H(i-1,j-1) + PAM(a_i,b_j)    (diagonal)

H(i,j) = MAX of | H(i-1,j) + gappenalty (up) | H(i,j-1) + gappenalty (left) | 0

The PAM matrix is the amino acid substitution matrix that encode the expected evolutionary change at the amino acid level.

To obtain the optimum local alignment, we start with the highest value in the matrix (i,j). Then, we go backwards to one of positions (i − 1,j), (i, j − 1), and (i − 1, j − 1) depending on the direction of movement used to construct the matrix.

Author
Javier Fresno
Date
June 2013

Hitmap Sequential version for the Smith-Waterman algorihtm. The Smith–Waterman algorithm performs local sequence alignment of protein sequences.

This version assumes a linear gap penalty. This algorithm creates the matrix H as follows:

              | H(i-1,j-1) + PAM(a_i,b_j)    (diagonal)

H(i,j) = MAX of | H(i-1,j) + gappenalty (up) | H(i,j-1) + gappenalty (left) | 0

The PAM matrix is the amino acid substitution matrix that encode the expected evolutionary change at the amino acid level.

To obtain the optimum local alignment, we start with the highest value in the matrix (i,j). Then, we go backwards to one of positions (i − 1,j), (i, j − 1), and (i − 1, j − 1) depending on the direction of movement used to construct the matrix.

Author
Javier Fresno
Date
June 2013

Definition in file SWseq.c.

Macro Definition Documentation

#define h (   i,
 
)    (hit_tileElemAtNoStride(H,2,i,j))

Definition at line 99 of file SWseq.c.

#define xback (   i,
 
)    (hit_tileElemAtNoStride(xTraceback,2,i,j))

Definition at line 104 of file SWseq.c.

#define yback (   i,
 
)    (hit_tileElemAtNoStride(yTraceback,2,i,j))

Definition at line 105 of file SWseq.c.

Function Documentation

int main ( int  argc,
char *  argv[] 
)

Main function.

< Time init

< Time computation

< Accumulate time in read

< Accumulate time in H matrix computation

< Accumulate time in backtracking

Definition at line 133 of file SWseq.c.

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void phase_comp_back ( )

Compute the traceback

void phase_comp_hmatrix ( )

Calculate the similarity matrix (H)

void phase_read_sequences ( )

Read the protein sequences

Variable Documentation

HitTile_h_t H

Definition at line 98 of file SWseq.c.

int match_length

Definition at line 120 of file SWseq.c.

int match_length1

Definition at line 121 of file SWseq.c.

int match_length2

Definition at line 122 of file SWseq.c.

int match_pos

Definition at line 125 of file SWseq.c.

HitTile_aa_t out1

Definition at line 108 of file SWseq.c.

HitTile_aa_t out2

Definition at line 109 of file SWseq.c.

HitTile_aa_t p1

Definition at line 94 of file SWseq.c.

HitTile_aa_t p2

Definition at line 95 of file SWseq.c.

int xBegin

Definition at line 116 of file SWseq.c.

int xMax

Definition at line 112 of file SWseq.c.

HitTile_trace_t xTraceback

Definition at line 102 of file SWseq.c.

int yBegin

Definition at line 117 of file SWseq.c.

int yMax

Definition at line 113 of file SWseq.c.

HitTile_trace_t yTraceback

Definition at line 103 of file SWseq.c.