/*>int align(char *seq1, int length1, char *seq2, int length2,
BOOL verbose, BOOL identity, int penalty,
char *align1, char *align2, int *align_len)
-----------------------------------------------------------
Input: char *seq1 First sequence
int length1 First sequence length
char *seq2 Second sequence
int length2 Second sequence length
BOOL verbose Display N&W matrix
BOOL identity Use identity matrix
int penalty Gap insertion penalty value
Output: char *align1 Sequence 1 aligned
char *align2 Sequence 2 aligned
int *align_len Alignment length
Returns: int Alignment score (0 on error)
Perform simple N&W alignment of seq1 and seq2. No window is used, so
will be slow for long sequences.
A single gap penalty is used, so gap extension incurrs no further
penalty.
Note that you must allocate sufficient memory for the aligned
sequences.
The easy way to do this is to ensure that align1 and align2 are
of length (length1+length2).
06.03.00 Implemented as a wrapper to affinealign() which is the old
align() routine, plus support for affine gap penalties,
plus new traceback code based on storing the path as we
go
*/
int align(char *seq1,
int length1,
char *seq2,
int length2,
BOOL verbose,
BOOL identity,
int penalty,
char *align1,
char *align2,
int *align_len)
{
return(affinealign(seq1, length1, seq2, length2, verbose, identity,
penalty, 0, align1, align2, align_len));
}
int main(int argc, char **argv)
{
char seq1[] = "ACTCLMCT",
seq2[] = "ACTCCT",
align1[100],
align2[100];
int score, al_len;
int i, j;
ReadMDM("pet91.mat");
for(i=0; i<sMDMSize; i++)
{
printf(" %c", sMDM_AAList[i]);
}
printf("\n");
for(i=0; i<sMDMSize; i++)
{
for(j=0; j<sMDMSize; j++)
{
printf("%3d", sMDMScore[i][j]);
}
printf("\n");
}
score = affinealign(seq1, strlen(seq1), seq2, strlen(seq2),
TRUE, FALSE,
10, 1, align1, align2, &al_len);
align1[al_len] = '\0';
align2[al_len] = '\0';
printf("%s\n", align1);
printf("%s\n", align2);
return(0);
}
