Detecting common amino acid sequence patterns with a gap

Abstract

We have developed a program GAPE (Gap Allowing Pattern Explorer) to extract amino acid sequence motifs conserved among distantly related proteins. The GAPE program is designed to allow a gap in the sequences. When the program is applied to some ligand-related consensus sequences, motifs extracted with low expectation of occurrence contain some of the amino acid residues chemically proved to be involved in the ligand recognition.