Hitmap 1.3
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Go to the source code of this file.
Macros | |
#define | h(i, j) (H[((i)*(size[1]+1))+(j)]) |
#define | xback(i, j) (xTraceback[((i)*(size[1]+1))+(j)]) |
#define | yback(i, j) (yTraceback[((i)*(size[1]+1))+(j)]) |
Functions | |
void | phase_read_sequences () |
void | phase_comp_hmatrix () |
void | phase_comp_back () |
int | main (int argc, char *argv[]) |
Variables | |
aa_t * | p1 |
aa_t * | p2 |
h_t * | H |
trace_t * | xTraceback |
trace_t * | yTraceback |
aa_t * | out1 |
aa_t * | out2 |
int | xMax |
int | yMax |
int | xBegin |
int | yBegin |
int | match_length |
int | match_length1 |
int | match_length2 |
int | match_pos |
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_ref.c.
Definition at line 102 of file SWseq_ref.c.
#define xback | ( | i, | |
j | |||
) | (xTraceback[((i)*(size[1]+1))+(j)]) |
Definition at line 107 of file SWseq_ref.c.
#define yback | ( | i, | |
j | |||
) | (yTraceback[((i)*(size[1]+1))+(j)]) |
Definition at line 108 of file SWseq_ref.c.
int main | ( | int | argc, |
char * | argv[] | ||
) |
Main function.
< Time init start
< Time init end
< Time computation start
< Time computation end
< Aux start timer for phases
< Aux end timer for phases
< Accumulate time in read
< Accumulate time in H matrix computation
< Accumulate time in backtracking
Definition at line 134 of file SWseq_ref.c.
void phase_comp_back | ( | ) |
Compute the traceback
void phase_comp_hmatrix | ( | ) |
Calculate the similarity matrix (H)
void phase_read_sequences | ( | ) |
Read the protein sequences
h_t* H |
Definition at line 101 of file SWseq_ref.c.
int match_length |
Definition at line 123 of file SWseq_ref.c.
int match_length1 |
Definition at line 124 of file SWseq_ref.c.
int match_length2 |
Definition at line 125 of file SWseq_ref.c.
int match_pos |
Definition at line 128 of file SWseq_ref.c.
aa_t* out1 |
Definition at line 111 of file SWseq_ref.c.
aa_t* out2 |
Definition at line 112 of file SWseq_ref.c.
aa_t* p1 |
Definition at line 97 of file SWseq_ref.c.
aa_t* p2 |
Definition at line 98 of file SWseq_ref.c.
int xBegin |
Definition at line 119 of file SWseq_ref.c.
int xMax |
Definition at line 115 of file SWseq_ref.c.
trace_t* xTraceback |
Definition at line 105 of file SWseq_ref.c.
int yBegin |
Definition at line 120 of file SWseq_ref.c.
int yMax |
Definition at line 116 of file SWseq_ref.c.
trace_t* yTraceback |
Definition at line 106 of file SWseq_ref.c.