Dear BrowserUK,
I was trying your code above with this set of strings: 
my @inst = ( 'CAGGTG',
             'CAGGTG' );

my $res1 = get_pwm(@inst);

[download]
But why it returns this answer: 
$VAR1 = {
    'A' => [ 0, '1' ],
    'T' => [ 0, 0, 0, 0, '1' ],
    'C' => [ '1' ],
    'G' => [ 0, 0, '1', '1', 0, '1' ]
};

[download]
Instead of the correct 
$VAR1 = {
    'A' => [ '0', '1', '0', '0', '0', '0' ],
    'T' => [ '0', '0', '0', '0', '1', '0' ],
    'C' => [ '1', '0', '0', '0', '0', '0' ],
    'G' => [ '0', '0', '1', '1', '0', '1' ] 
};

[download]
It seems that the code didn't supply 0 when the bases is not present in a particular column as it should after it found 1.
I thought from this line of the code should do that job, but seems not. 
    @$_ = map { $_ ? $_ / $n : 0 } @$_ for values %pwm;

[download]
Please advice.

---
neversaint and everlastingly indebted.......

In reply to Re^4: Position Weight Matrix of Set of Strings by neversaint
in thread Position Weight Matrix of Set of Strings by monkfan

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