Approximate P-Values for Local Sequence Alignments: Numerical Studies

Publisher Website
Google Scholar
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.

This publication has 19 references indexed in Scilit: