BOL: Needleman-Wunsch Algorithm in Perl

BioScripts
Radha Agarkar
Needleman-Wunsch Algorithm in Perl
Needleman-Wunsch Algorithm in Perl

#!/usr/bin/perl

# USAGE:   perl nw.pl HEAGAWGHEE PAWHEAE BLOSUM50.txt -8

# See:     "Biological sequence anaysis" Durbin et al. ed. CUP 1998, Pg. 19
# Needleman-Wunsch global alignment algo (GOTHO 1982 mod)

# usage statement
die "usage: $0 <sequence 1> <sequence 2> <substmatrix> <gapscore> \n" unless @ARGV == 4;

# get sequences, matrix and gapcost from command line
my ($seq1, $seq2, $smfile, $gapcost) = @ARGV;

# scoring scheme (instead of using fixed MATCH and MISMATCH scores we will use values read from BLOSUM50)
my $MATCH    =  1; # +1 for letters that match
my $MISMATCH = -1; # -1 for letters that mismatch
my $GAP      = $gapcost; # for any gap
my %BLOSUM50 = ();
my @aalist = ();

# read substitution matrix
open in, $smfile;
while(<in>){
    if($.<2){next;}
    # read columns names (aa)
    if($.<3){
        chop $_;
        @aalist=split(/\s+/,$_);
        next;
        }
    chop $_;
    @vals=split(/\s+/,$_);
    $curaaROW=$vals[0];
    for($i=1;$i<=$#vals;$i++){
        $curaaCOLUMN=$aalist[$i];
        $BLOSUM50{$curaaROW}{$curaaCOLUMN}=$vals[$i];
    }   
}
close in;


# 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}   = $GAP * $j;
    $matrix[0][$j]{pointer} = "left";
}
for (my $i = 1; $i <= length($seq2); $i++) {
    $matrix[$i][0]{score}   = $GAP * $i;
    $matrix[$i][0]{pointer} = "up";
}

# fill
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} + $BLOSUM50{$letter1}{$letter2};
        }
        else {
            $diagonal_score = $matrix[$i-1][$j-1]{score} + $BLOSUM50{$letter1}{$letter2};
        }

        # calculate gap scores
        $up_score   = $matrix[$i-1][$j]{score} + $GAP;
        $left_score = $matrix[$i][$j-1]{score} + $GAP;

        # 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";
            }
        }
    }
}

# trace-back

my $align1 = "";
my $align2 = "";
my $descrstr = "";

# start at last cell of matrix
my $j = length($seq1);
my $i = length($seq2);

while (1) {
    last if $matrix[$i][$j]{pointer} eq "none"; # ends at first cell of matrix

    if ($matrix[$i][$j]{pointer} eq "diagonal") {
        $align1 .= substr($seq1, $j-1, 1);
        $align2 .= substr($seq2, $i-1, 1);
        if(substr($seq1, $j-1,1) eq substr($seq2, $i-1,1)){$descrstr .="|";}else{$descrstr .= ".";}
        $i--;
        $j--;
    }
    elsif ($matrix[$i][$j]{pointer} eq "left") {
        $align1 .= substr($seq1, $j-1, 1);
        $align2 .= "-";
        $descrstr .= " ";
        $j--;
    }
    elsif ($matrix[$i][$j]{pointer} eq "up") {
        $align1 .= "-";
        $align2 .= substr($seq2, $i-1, 1);
        $descrstr .= " ";
        $i--;
    }    
}

$align1 = reverse $align1;
$align2 = reverse $align2;
$descrstr = reverse $descrstr;

# print matrices:
print "\n\n";

for(my $i = 0; $i <= length($seq2); $i++) {
    for(my $j = 0; $j <= length($seq1); $j++) {
        printf("%2.1f", $matrix[$i][$j]{score});
        print("\t");
    }
    print"\n";
}
print "\n\n";

# print the alignment:
print "$align1\n";
print "$descrstr\n";
print "$align2\n";

__END__
# Entries for the BLOSUM50 matrix at a scale of ln(2)/3.0.
Find matrix at http://bioinformaticsonline.com/file/view/27455/blosum50-matrix
BOL

Radha Agarkar

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Needleman-Wunsch Algorithm in Perl
