Robust E-Values for Gapped Local Alignments

Abstract

We examine a Poisson heuristic for judging the significance of local sequence alignments with gaps. Model parameters are estimated directly from the sequences to be aligned, so that laborious prior simulation studies or database comparisons for the estimation of parameters describing the connection between score and E-value are unnecessary. Simulation studies give evidence that this method gives reasonable results even when the usual assumptions like the independence of sequence positions are violated.