Summation test for gap penalties and strong law of the local alignment score

DOI10.1214/105051605000000061zbMATH Open1070.92037arXivmath/0505247OpenAlexW3099655049MaRDI QIDQ558686FDOQ558686

Hock Peng Chan

Publication date: 13 July 2005

Published in: The Annals of Applied Probability (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/math/0505247

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.

zbMATH Keywords

large deviationscomputational biologyDNA sequencingsequence alignmentlog moment generating functions

Mathematics Subject Classification ID

Large deviations (60F10) Protein sequences, DNA sequences (92D20) Strong limit theorems (60F15) Computational methods for problems pertaining to biology (92-08)

Cites Work

• Biological Sequence Analysis
• Sequence comparison with concave weighting functions
• A phase transition for the score in matching random sequences allowing deletions
• Limit distribution of maximal non-aligned two-sequence segmental score
• Upper bounds and importance sampling of \(p\)-values of DNA and protein sequence alignments
• Critical phenomena for sequence matching with scoring
• A limit theorem for matching random sequences allowing deletions

Cited In (2)

• Inequalities for the score constant in matching random sequences
• Maximum-likelihood estimation of the statistical distribution of Smith- Waterman local sequence similarity scores

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