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ezekiel
<p>Your problem is very similar to protein sequence homology searches. A protein can be represented as nothing more than a string from an alphabet of 20 letters. Sequence homology searches (which are crucial to biology and bioinformatics) basically attempt to find and score similarities between two or more such sequences.
<p>Various algorithms exist to do this e.g. Needleman and Wunsch (Journal of Molecular Biology <strong>48</strong> pp443) and the ever popular BLAST <a href="http://www.ncbi.nlm.nih.gov/blast">www.ncbi.nlm.nih.gov/blast</a>
Of course these solutions are designed for molecular biology and would require a lot of work to alter them to handle general strings. My guess is you are looking for a simpler solution...
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