Temple F. Smith coauthored the algorithm for finding maximally similar segments within longer molecular sequences, now known as the Smith-Waterman algorithm. Its dynamic programming table permits a fresh start at score zero; a high-scoring segment can therefore begin and end inside either input rather than being forced to span both entire sequences.[ref]
Identification of common molecular subsequences by Temple F. Smith and Michael S. Waterman. Algorithm, equation 1 and traceback description, printed pp. 195–196
The zero option is a mechanistic part of the optimization: it discards a sufficiently unfavorable preceding alignment. Alignment traceback begins at a largest table entry and ends at zero. This supports finding a conserved region embedded within otherwise different sequences; the resulting similarity still requires biological interpretation rather than automatically proving a particular evolutionary history.
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