Approximate P-values for local sequence alignments: Numerical studies

J. D. Storey, D. Siegmund

Research output: Contribution to journalArticlepeer-review

22 Scopus citations


Siegmund and Yakir (2000) have given an approximate p-value when two independent, identically distributed sequences from a finite alphabet are optimally aligned based on a scoring system that rewards similarities according to a general scoring matrix and penalizes gaps (insertions and deletions). The approximation involves an infinite sequence of difficult-to-compute parameters. In this paper, it is shown by numerical studies that these reduce to essentially two numerically distinct parameters, which can be computed as one-dimensional numerical integrals. For an arbitrary scoring matrix and affine gap penalty, this modified approximation is easily evaluated. Comparison with published numerical results show that it is reasonably accurate.

Original languageEnglish (US)
Pages (from-to)549-556
Number of pages8
JournalJournal of Computational Biology
Issue number5
StatePublished - 2001
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Computational Mathematics
  • Genetics
  • Molecular Biology
  • Computational Theory and Mathematics
  • Modeling and Simulation


  • Affine gap penalty
  • Local alignment
  • Markov renewal theory
  • p-value


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