Summation test for gap penalties and strong law of the local alignment score
Hock Peng Chan
Abstract
A summation test is proposed to determine admissible types of gap penalties for logarithmic growth of the local alignment score. We also define a converging sequence of log moment generating functions that provide the constants associated with the large deviation rate and logarithmic strong law of the local alignment score and the asymptotic number of matches in the optimal local alignment.
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