JaMBW Chapter 3.1.7
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:
- Sequence input
- Symbols used
Either paste or type in the top area the sequence of interes, using one letter notation. Any
character or symbol that does not belong to the IUPAC-IUB set is
- removal of header information
Only the sequence must be placed in the top window:
heading comments must be removed
- long sequences and small window
In order to allow users with small screens to still be able of use this
program, the size of each window had been made rather small. Therefore,
use the scroll-bars in order to move around in the input and output windows.
The suggested strategy is to double click in the specified area and then
do copy/paste from/to the text-editor of choice or across different
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.
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