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Fold topologies are not only shared by proteins that have similar functions and clearly related sequences, but also by proteins with very different functions and possibly unrelated sequences (using standard sequence comparison techniques). Thus the classification of protein structures is a separate, yet overlapping, task to that of sequence classification (see Section 1.4.1). Sequence classification depends upon sequence comparison, usually via pairwise alignments of amino acid sequences. By analogy, most structural classifications are based upon pairwise structural alignments. In order to best explain this concept, the general principles of the commonly used dynamic programming alignment algorithm are presented below.