New approximate P-value of gapped local sequence alignments

DOI10.1016/J.CRMA.2007.11.022MaRDI QIDQ2473023zbMATH OpenOpenAlexFDO

Authors Afshin M. Fayyaz, Louis Ferré, Claudie Hassenforder, Sabine Mercier

Publication date 26 February 2008

Published in Comptes Rendus. Mathématique. Académie des Sciences, Paris (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.crma.2007.11.022

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40)

Recommendations

• H-tuple approach to evaluate statistical significance of biological sequence comparison with gaps
• Approximate p-values for local sequence alignments.
• Research in Computational Molecular Biology
• Toward an accurate statistics of gapped alignments
• Upper bounds and importance sampling of \(p\)-values of DNA and protein sequence alignments

Cites work

• A limit theorem for matching random sequences allowing deletions
• Approximate p-values for local sequence alignments.
• H-tuple approach to evaluate statistical significance of biological sequence comparison with gaps
• Limit distribution of maximal non-aligned two-sequence segmental score
• Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.

Cited in

(8)

• Upper bounds and importance sampling of \(p\)-values of DNA and protein sequence alignments
• Approximate p-values for local sequence alignments.
• Extending alignments with k-mismatches and -gaps
• The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods
• SEPA: Approximate Non-subjective Empirical p-Value Estimation for Nucleotide Sequence Alignment
• Robust k-mer frequency estimation using gapped k-mers
• H-tuple approach to evaluate statistical significance of biological sequence comparison with gaps
• Research in Computational Molecular Biology

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