Abstract
The major outlines of an exhaustive algorithm which discovers the optimal correspondence of a pair of code strings from a pre-specified alphabet is presented. The measure of the quality of correspondence is the information required to effect the mutations indicated by the correspondence. This formulation is shown to lead naturally to expressions for the penalty for introducing gaps, an ad hoc feature of previous approaches. The limitations of earlier algorithms of this type are delineated, and a non-trivial example of the matching of two partial sequences of Tyrosyl t-RNA from E. coli and Baker's yeast is given.
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