Protein map: an alignment-free sequence comparison method based on various properties of amino acids.

In this paper, we propose a new protein map which incorporates with various properties of amino acids. As a powerful tool for protein classification, this new protein map both considers phylogenetic factors arising from amino acid mutations and provides computational efficiency for the huge amount of data. The ten amino acid physico-chemical properties (the chemical composition of the side chain, two polarity measures, hydropathy, isoelectric point, volume, aromaticity, aliphaticity, hydrogenation, and hydroxythiolation) are utilized according to their relative importance. Moreover, during the course of calculation of genetic distances between pairs of proteins, this approach does not require any alignment of sequences. Therefore, the proposed model is easier and quicker in handling protein sequences than multiple alignment methods, and gives protein classification greater evolutionary significance at the amino acid sequence level.