Hitmap 1.3
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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 |
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.
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.
Definition in file SWseq.c.
#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)) |
int main | ( | int | argc, |
char * | argv[] | ||
) |
void phase_comp_back | ( | ) |
Compute the traceback
void phase_comp_hmatrix | ( | ) |
Calculate the similarity matrix (H)
void phase_read_sequences | ( | ) |
Read the protein sequences