Hi.

Here your version of the code corrected so that it works

print"Enter the mRNA Sequence\n";    
$count = 0;
$count1 = 0;
$seq = <>;
chomp($seq);
$p = '';
$ln = length($seq);
$j = $ln/3;
for($i=0,$k=0;$i<$ln,$k<$j;$k++)
{
    $fra[$k]=substr($seq,$i,3);
    $i=$i+3;
    print "$k -> @fra\n";
    print "$k -> {$fra[$k]}\n";
    if($fra[$k] eq 'AGA')
    {
        $count++;
        print"The number of AGA is $count\n";
    }
    elsif($fra[$k] eq 'UUU')
    {
        $count1++;
        print" The number of UUU is $count1\n";
    }
}

With some printing here and there to show you what is going on.

The main problem was that you compare {$fra[$k]} with UUU, but {$fra[$k]} is {UUU} (including braces)

Here a shorter version, possibly easier to read

use strict;
print"Enter the mRNA Sequence\n";

my $seq = <>;
chomp($seq);
my %freq;

my @codons = split(/(\w{3})/, $seq);
foreach my $thisCodon (@codons) {
    $freq{$thisCodon}++;
}

print "AGA found $freq{'AGA'} times\n";
print "UUU found $freq{'UUU'} times\n";

Hi there,

Bioperl has the Bio::Tools::SeqWords module which already implements a solution to this problem for an arbitrary word size. It can handle overlapping words too. Just check the code to see how it works.

The program should find the substrings in a given string and count their number of occurrences.

I don't know whether that's relevant to you at all, but if this is for speed/efficiency and/or must handle lots of data and/or you need repeated lookups, I'd recommend using a suffix array approach to substring searching. There is obviously a cost to building the suffix array in the first place, but once you have it, locating substrings is very fast.

This includes overlapping codons:

use strict;
use warnings;
my $string="AGAUUUAGA";
my @trinucs=($string=~/(?=(.{3}))/g);
my %tri_count=();
$tri_count{$_}++ for @trinucs;
print $_,":",$tri_count{$_},"\n" for sort keys(%tri_count);

Output is:

AGA:2
AUU:1
GAU:1
UAG:1
UUA:1
UUU:1