Analysis of data from experimentally determined antigenic sites on proteins has revealed that the hydrophobic residues Cys, Leu and Val, if they occur on the surface of a protein, are more likely to be a part of antigenic sites. A semi-empirical method which makes use of physicochemical properties of amino acid residues and their frequencies of occurrence in experimentally known segmental epitopes was developed by Kolaskar and Tongaonkar to predict antigenic determinants on proteins. This method is based on a single parameter and thus very simple to use. Here is a sample session with antigenic. By using the '-featout' qualifier, a GFF file of the predicted regions can be produced.
Users can provide their own data files in their own directories.
A semi-empirical method for prediction of antigenic determinants on protein antigens. The program will warn you if the sequence is not a protein or has ambiguity codes. It exits with status 0, unless a region is badly constructed. Known bugs None. This program is intended to be used by everyone and everything, from naive users to embedded scripts.