Abstract
The method of quantifying protein sequences by application of principal component analysis has been improved to detect the similarity by numerical criteria. The alignment of sequences that are quantified as the first principal components which reflect the physicochemical properties of constituent amino acid residues, is searched by the information on residue variety in the sequencs as well as the resemblance of the properties. The ability of newly developed method is tested by two known but obscure motifs and is also discussed with reference to usual methods for similarity search.
