Pattern driven algorithms
Brute force - enumerate all patterns (for instance, all substrings) up to a given length (complexity)
Evaluate their fitness with respect to the input sequences and output the best
Unrealistic for patterns of even modest size even for substring patterns (e.g., for substring patterns of length 10 over the amino acid alphabet, there are more than 1013 different substrings to enumerate in this way)
E.g. PRATT program (Jonassen, U.Bergen, via www.ebi.ac.uk)