BioPerl won't help you with this problem, it not being a biological question beyond using residue symbols.
If i understand correctly though, you want the maximum number of 4 character tuples?
Then you could try some kind of search path algorithm, and then compare the different paths for the longest?
You would have to have some way of remembering your searchpath, splitting the path every time you come across somewhere where you could take alternate routes? You have some simple rules already, like if two sequential letters are the same you can either form an 'AAAA' type tuple or an 'ABCD' type, etc...

There is a lot of info on search path / graph search algorithms in wikipedia etc... e.g. http://en.wikipedia.org/wiki/Dijkstra's_algorithm you just want the opposite of what they usually do...

I would be interested in seeing what you come up with

Just a something something...

In reply to Re: finding tuples by BioLion
in thread finding tuples by Anonymous Monk

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