JaMBW Chapter 3.1.7

Antigenicity Plot


Given a sequence of aminoacids, this program computes and plots the antigenicity along the polypeptide chain, as predicted by the algorithm of Hopp and Woods (1981).

Mode of operation

The program uses 3 windows: the top one should be filled from the user, with the sequence of interest, the small window beneath is used by the program to return messages, while the bottom one visualizes the results of the analysis. The following steps must be performed to use this program:
  1. Sequence input
  2. Compute
    Once the sequence is placed in the top window, by pressing the "COMPUTE" button the antigenic index is computed at each aminoacid position, and then visualized.

A Java-enabled browser would have in this place a window similar to this picture:

How to understand its output

The chart displays the variation of the antigenic index as function of aminoacid position. The higher the antigenic index, the more likely should be that antibodies would "see" those groups of residues.


Author:Luca I.G. TOLDO, based on a C code provided by Ramu Chenna Edition date: 28 February 1997