title: Approximate p-values for local sequence alignments: numerical studies.
abstract: 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.
authors.affiliation: Department of Statistics, Stanford University, Stanford, CA 94305, USA.
authors.forename: J D
authors.initials: JD
authors.lastname: Storey
authors.forename: D
authors.initials: D
authors.lastname: Siegmund
mesh_terms: D008958:Models, Molecular; D016415:Sequence Alignment / Q000379:methods*