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A general method for comparing two macromolecules is developed. The method differs from more traditional procedures in that matches are evaluated dependent on sequence context. We first define a context dependent similarity score between sequences and give a dynamic programming algorithm for its calculation. Conditions are then described which allow the conversion of the similarity score to a metric distance. The class of metrics obtained in this manner includes the Sellers metric. An advantage of the method is the ability to make very rapid comparisons and to align long sequences.
Wilbur et al. (Fri,) studied this question.