Binary Assignments of Amino Acids from Pattern Conservation
Abstract
Description
We develop a simple optimization procedure for assigning binary values to the amino acids. The binary values are determined by a maximization of the degree of pattern conservation in groups of closely related protein sequences. The maximization is carried out at fixed composition. For compositions approximately corresponding to an equipartition of the residues, the optimal encoding is found to be strongly correlated with hydrophobicity. The stability of the procedure is demonstrated. Our calculations are based upon sequences in the SWISS-PROT database.
9 pages, 4 Postscript figures. References and figure added
9 pages, 4 Postscript figures. References and figure added