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Perl script for Smith-Waterman Algorithm (local alignment)

# 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";