My most respected monks,
I am looking a way to find consensus string from given set of strings (length is assumed to be the same within the set). Basically consensus string mean single string that represent most common occurence from the given set. Here is the example of it: 
           Set 1:                         Set 2:
           AAAAA                          AAAAA
           ATCGA                          AACGA
           ATAAA                          ATAAA
                                          ATAAA
Consensus: ATAAA             Consensus:  A[AT]AAA

Note: like Set 2, there can be other cases that has
more than two consensus in a particular position.
They need to be captured within square bracket [].

[download]
Below is my incredibly naive, inefficient and inflexible code. There are two issues which I still unable to solve here:
So here I am again, humbly seeking for your wisdom.

My current code:
use strict;
use warnings;

my @instances = qw ( 
                     AAAAA
                     ATCGA
                     ATAAA
                 );
my @instances2 = qw ( 
                     AAAAA
                     AACGA
                     ATAAA
                     ATAAA
                 );

print consensus(@instances),"\n";

sub consensus{
 my @mi = @_;
 my $motif_count=0;
 my @words =();
 my $L = undef;

  my  @A = ();
  my  @T = ();
  my  @C = ();
  my  @G = ();

  my  $a = 0;
  my  $c = 0;
  my  $g = 0;
  my  $t = 0;
  my  $w = 0;

    foreach my $mi ( @mi ) {
        chomp($mi);
        $mi =~ s/\s//g;

        $w = length($mi);

        #for motif instances count
        @words = split( /\W+/, $mi );
        $motif_count += @words;
      }

         for ( my $j = 0 ; $j < $w ; $j++ ) {

        # Initialize the base counts.
        my $L =0;
        foreach my $mi ( @mi ) {
            chomp($mi);
            my $L = $mi;
            my $sb = substr( $L, $j, 1 );
            while ( $sb =~ /a/ig ) { $a++ }
            while ( $sb =~ /t/ig ) { $t++ }
            while ( $sb =~ /c/ig ) { $c++ }
            while ( $sb =~ /g/ig ) { $g++ }

        }
        push( @A, $a );
        push( @T, $t );
        push( @C, $c );
        push( @G, $g );

        $a = 0;
        $c = 0;
        $g = 0;
        $t = 0;

    }

    my @cons = ();
    #print "$w\n";
    for (my $b=0; $b <$w ;$b++) {

        if ( $A[$b] > $T[$b] && $A[$b] > $C[$b] && $A[$b] > $G[$b] ) {
            push( @cons, 'A');
        }

        elsif ( $T[$b] > $C[$b] && 
                $T[$b] > $A[$b] && 
                $T[$b] > $G[$b] ) {
            push( @cons, 'T' );
        }

        elsif ( $C[$b] > $G[$b] && 
                $C[$b] > $A[$b] && 
                $C[$b] > $T[$b] ) {
            push( @cons, 'C' );
        }
      elsif ( $G[$b] > $A[$b] && 
                $G[$b] > $C[$b] && 
                $G[$b] > $T[$b] ) {
            push( @cons, 'G' );
        }
        elsif ( $A[$b] = $T[$b] ) {
            push( @cons, 'T' );
        }
        elsif ( $A[$b] = $G[$b] ) {
            push( @cons, 'G' );
        }
        elsif ( $A[$b] = $C[$b] ) {
            push( @cons, 'C' );
        }
        elsif ( $T[$b] = $C[$b] ) {
            push( @cons, 'C' );
        }
        elsif ( $T[$b] = $G[$b] ) {
            push( @cons, 'G' );
        }
        else { push @cons, 'G'; }


    }

    return @cons;
}

[download]

Regards,
Edward

In reply to Finding Consensus String by monkfan

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