Journal
JOURNAL OF COMPUTATIONAL BIOLOGY
Volume 8, Issue 5, Pages 549-556Publisher
MARY ANN LIEBERT INC PUBL
DOI: 10.1089/106652701753216530
Keywords
local alignment; affine gap penalty; p-value; Markov renewal theory
Ask authors/readers for more resources
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
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available