# Smith-Waterman Algorithm
# usage statement
die "usage: $0 <sequence 1> <sequence 2>\n" unless @ARGV == 2;
# get sequences from command line
my ($seq1, $seq2) = @ARGV;
# scoring scheme
my $MATCH = 1; # +1 for letters that match
my $MISMATCH = -1; # -1 for letters that mismatch
my $GAP = -1; # -1 for any gap
# initialization
my @matrix;
$matrix[0][0]{score} = 0;
$matrix[0][0]{pointer} = "none";
for(my $j = 1; $j <= length($seq1); $j++) {
$matrix[0][$j]{score} = 0;
$matrix[0][$j]{pointer} = "none";
}
for (my $i = 1; $i <= length($seq2); $i++) {
$matrix[$i][0]{score} = 0;
$matrix[$i][0]{pointer} = "none";
}
# fill
my $max_i = 0;
my $max_j = 0;
my $max_score = 0;
for(my $i = 1; $i <= length($seq2); $i++) {
for(my $j = 1; $j <= length($seq1); $j++) {
my ($diagonal_score, $left_score, $up_score);
# calculate match score
my $letter1 = substr($seq1, $j-1, 1);
my $letter2 = substr($seq2, $i-1, 1);
if ($letter1 eq $letter2) {
$diagonal_score = $matrix[$i-1][$j-1]{score} + $MATCH;
}
else {
$diagonal_score = $matrix[$i-1][$j-1]{score} + $MISMATCH;
}
# calculate gap scores
$up_score = $matrix[$i-1][$j]{score} + $GAP;
$left_score = $matrix[$i][$j-1]{score} + $GAP;
if ($diagonal_score <= 0 and $up_score <= 0 and $left_score <= 0) {
$matrix[$i][$j]{score} = 0;
$matrix[$i][$j]{pointer} = "none";
next; # terminate this iteration of the loop
}
# choose best score
if ($diagonal_score >= $up_score) {
if ($diagonal_score >= $left_score) {
$matrix[$i][$j]{score} = $diagonal_score;
$matrix[$i][$j]{pointer} = "diagonal";
}
else {
$matrix[$i][$j]{score} = $left_score;
$matrix[$i][$j]{pointer} = "left";
}
} else {
if ($up_score >= $left_score) {
$matrix[$i][$j]{score} = $up_score;
$matrix[$i][$j]{pointer} = "up";
}
else {
$matrix[$i][$j]{score} = $left_score;
$matrix[$i][$j]{pointer} = "left";
}
}
# set maximum score
if ($matrix[$i][$j]{score} > $max_score) {
$max_i = $i;
$max_j = $j;
$max_score = $matrix[$i][$j]{score};
}
}
}
# trace-back
my $align1 = "";
my $align2 = "";
my $j = $max_j;
my $i = $max_i;
while (1) {
last if $matrix[$i][$j]{pointer} eq "none";
if ($matrix[$i][$j]{pointer} eq "diagonal") {
$align1 .= substr($seq1, $j-1, 1);
$align2 .= substr($seq2, $i-1, 1);
$i--; $j--;
}
elsif ($matrix[$i][$j]{pointer} eq "left") {
$align1 .= substr($seq1, $j-1, 1);
$align2 .= "-";
$j--;
}
elsif ($matrix[$i][$j]{pointer} eq "up") {
$align1 .= "-";
$align2 .= substr($seq2, $i-1, 1);
$i--;
}
}
$align1 = reverse $align1;
$align2 = reverse $align2;
print "$align1\n";
print "$align2\n";
