Dear Monks,
I am trying to construct all possible strings from 4 bases (ATCG), there are 4 ^ L possible strings of such.

E . g with L = 2 we have AA, AT, AC, AG, .. GC, GA, GT, GG as many as 4 ^ 2 = 16 strings,
with L = 3 we have as many as 4 ^ 3 = 64 strings

What's wrong with my code below ? Such that it doesnt give what I want ?
Thanks so much before hand .

 #!/usr/bin/perl -w
use strict;
use warnings;
use Data::Dumper;

my $l = 2;    #Motif Length

my @cand_motif;

my $all_a = 'A' x $l;
my $all_t = 'T' x $l;
my $all_c = 'C' x $l;
my $all_g = 'G' x $l;

my @initial_motifs = ( $all_a, $all_t, $all_c, $all_g );

my @enumerated_motifs;

my (@nucleotides) = ( 'a', 't', 'c', 'g' );

foreach my $cand_motif (@initial_motifs) {

    for ( my $i = 0 ; $i < $l ; $i++ ) {

        foreach my $nucl (@nucleotides) {

            substr( $cand_motif, $i, 1 ) = $nucl;
            push @enumerated_motifs, $cand_motif;

            #print "$cand_motif\n";
        }

    }
}

my $count = @enumerated_motifs;
print "Count = $count\n";
print Dumper \@enumerated_motifs;

[download]
Regards,
Edward

In reply to Trying to construct all possible strings from 4 bases [ATCG] by monkfan

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