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  • Needleman-Wunsch perl script

    Dear all,
    Actually i posted a similar question on Biostars about usage of Needleman perl module.
    i have problem with the following script (kind helps from a biostars member). Could anyone help to correct it? THANKS A LOT!
    My ideal output is:
    HTML Code:
    CTAT-------CTA   CTATTTTTTTTCTG   -9
    However, the following script produces the below result
    HTML Code:
    CTATCTA   CTATTTTTTTTCTG   -9
    script:
    HTML Code:
    #!/usr/bin/env perl
    use strict;
    use warnings;
    use Algorithm::NeedlemanWunsch;
    ### scoring function:
    sub score_sub {
      if (!@_) {
        return -2;            # gap penalty
      }
      ## mismatch scores -1, match +1
      return ($_[0] eq $_[1]) ? 1 : -1;
    }
    
    my $a = "ATCTATC";
    my $b = "GTCTTTTTTTTATC";
    my @a = split //, $a; # make an array
    my @b = split //, $b;
    my ($a_align, $b_align);
    
    sub on_align  {  
    $a_align .= $a[$_[0]];
    $b_align .= $b[$_[1]];
    };
     
    sub on_shift_a { $a_align .= $a[$_[0]];};
    sub on_shift_b { $b_align .= $b[$_[0]];};
    
    sub on_select_align { print "(select_align)\n"; return (keys (%{$_[0]})) [0]};
    
    my $matcher = Algorithm::NeedlemanWunsch->new(\&score_sub);
    my $score = $matcher->align(
                    \@a,
                    \@b,
                    {   align     => \&on_align,
                    shift_a => \&on_shift_a,
                    shift_b => \&on_shift_b,
             # select_align => \&on_select_align
                    });
    
    print "$a_align\t$b_align\t";
    print "$score\n";

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