I've been known to reinvent wheels from time to time, but this particular wheel has been around the block a few times...

CPAN. Specifically Bio::Matrix::PSM::IO::masta. Per the docs, this module will

convert a set of aligned sequences: 
ACATGCAT
ACAGGGAT
ACAGGCAT
ACCGGCAT

[download]
to a PFM (SiteMatrix object)

Given the number of PFM-related modules within Bioperl I would imagine anything you want to do is already written.

Unfortunately I don't have time to provide an example. However, I would be very interested to see what you come up with if you go this route. Please post your solution when you are done so others can learn from your experience.

HTH

In reply to Re: To count letters (%identity) in DNA alignment by bobf
in thread To count letters (%identity) in DNA alignment by sedm1000

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