BrowserUk,
Given this set of sequences where base A doesn't exists (i.e, only CGT). 
my @inst = ( 'GGTGTGCC', 
             'GCTGTGGG', 
             'GGTGGGCC' );

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The code gives this matrix only: 
T => 0 0 1 0 0.666666666666667 0 0 0 
C => 0 0.333333333333333 0 0 0 0 0.666666666666667 0.666666666666667
G => 1 0.666666666666667 0 1 0.333333333333333 1 0.333333333333333 0.3
+33333333333333

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Note that it doesn't show matrix element of A: 
A => 0 0 0 0 0 0 0 0

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My question is how can I initialize your code above, so it can also includes matrix where the bases doesn't exist?
Given that there are only 4 alphabets [ATCG] required for the construction of matrix.

Regards,
Edward

In reply to Re^6: Position Weight Matrix of Set of Strings by monkfan
in thread Position Weight Matrix of Set of Strings by monkfan

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