Summation test for gap penalties and strong law of the local alignment score
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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.
Recommendations
- Proportion of Gaps and Fluctuations of the Optimal Score in Random Sequence Comparison
- A phase transition for the score in matching random sequences allowing deletions
- Inequalities for the score constant in matching random sequences
- An upper bound on the convergence rate of a second functional in optimal sequence alignment
- Approximate p-values for local sequence alignments.
Cites work
- A limit theorem for matching random sequences allowing deletions
- A phase transition for the score in matching random sequences allowing deletions
- Biological Sequence Analysis
- Critical phenomena for sequence matching with scoring
- Limit distribution of maximal non-aligned two-sequence segmental score
- Sequence comparison with concave weighting functions
- Upper bounds and importance sampling of \(p\)-values of DNA and protein sequence alignments
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