Motif-Biased Protein Sequence Alignment

Abstract

ABSTRACT

A method was developed for pairwise protein sequence alignment to emulate the effect of structural knowledge or multiple sequences. Runs of matches of the preferred length were emphasized through the use of a product-bias allowing short motifs to influence the alignment to a degree that was a realistic reflection of their infrequency of occurrence. This gave motifs a locally high scoring match, making their alignment relatively less sensitive to the value of the gap penalty. This property should be a great advantage when a large number of sequence comparisons are made with a fixed set of parameter values, as typically occurs in the scan of a sequence databank with a probe or in the development of a multiple alignment.