Antigenic

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ANTIGENIC

ANTIGENIC

FUNCTION

Antigenic looks for potential antigenic regions using the method of Kolaskar.

Antigenic predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar (1990); FEBS Letters 276:172-174 "A semi-empirical method for prediction of antigenic determinants on protein antigens."

AUTHOR

This program was written by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).

EXAMPLE

Here is a sample session with Antigenic

  
  
  % antigenic
  
   ANTIGENIC uses protein sequence data
  
   ANTIGENIC of what sequence ?  Sw:a1ag_human
  
                Start (* 1 *) ?
                End (* 201 *) ?
  
    What should I call the output file (* a1ag_human.anti *) ?
  
  %

OUTPUT

The output from Antigenic is a simple report of hits in the sequence.

  
  
  ANTIGENIC of sw:a1ag_human Check: 5478 from: 1 to: 201
  
  ID   A1AG_HUMAN     STANDARD;      PRT;   201 AA.
  AC   P02763;
  DT   21-JUL-1986 (REL. 01, CREATED)
  DT   01-JAN-1988 (REL. 06, LAST SEQUENCE UPDATE)
  DT   01-JUN-1994 (REL. 29, LAST ANNOTATION UPDATE)
  DE   ALPHA-1-ACID GLYCOPROTEIN 1 PRECURSOR (OROSOMUCOID) (OMD). . . .
  
  Length 201 residues, score calculated from 4 to 198
  
  Report all peptides over 6 residues
  
  Found 10 hits scoring over 1.00 (true average 1.03)
  Maximum length 30 at residues 4-33
  
   Sequence:  SWVLTVLSLLPLLEAQIPLCANLVPVPITN
         |                            |
         4                            33
  
   Entries in score order, max score at "*"
  
  (1) Score 1.208 length 30 at residue 4-33
                 *
   Sequence:  SWVLTVLSLLPLLEAQIPLCANLVPVPITN
         |                            |
         4                            33
  
     ////////////////////////////
  
  (10) Score 1.052 length 7 at residue 107-113
          *
   Sequence:  SRYVGGQ
         |     |
       107     113

ALGORITHM

Antigenic uses the method of Kolaskar and Tongaonkar (1990); FEBS Letters 276:172-174 "A semi-empirical method for prediction of antigenic determinants on protein antigens". In this paper, 169 antigenic determinants were experimentally determined. The 156 which have less than 20 amino acids per determinant were selected (total 2066 residues). f(Ag) was calculated as the frequency of occurrence of each residue in antigenic determinants [f(Ag) = Epitope_occurrence/2066]. The Hydrophilicity, Accessibility and Flexibility values are from Parker, Guo and Hodges (1986); Biochemistry 25:5425-5432. In a given protein, the average for each 7-mer is calculated, and values are assigned to the central residue the of 7-mer. A residue is considered to be on the surface if any of the 7-mer values was above the average for the protein. These results were used to obtain f(s) as the frequency of occurrence of amino acids at the surface.

Prediction algorithm:

1. Calculate the average propensity for each overlapping 7-mer and assign the result to the central residue (i+3) of the 7-mer.

2. Calculate the average for the whole protein.

3. (a) If the average for the whole protein is above 1.0 then all residues having above 1.0 are potentially antigenic.

3. (b) If the average for the whole protein is below 1.0 then all residues having above the average for the whole protein (note: the original paper has a mangled formula here) are potentially antigenic.

4. Find 6-mers where all residues are selected by step 3 above

INPUT FILE

The input file for Antigenic is a GCG protein sequence file.

COMMAND-LINE SUMMARY

All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  
  
  Minimum Syntax: % antigenic [-INfile=]Sw:a1ag_human -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=100           Range of interest
  [-OUTfile=]a1ag_human.anti  Output file
  
  Local Data Files:
  
  -DATa=kolaskar.dat          Antigenicity parameters for amino acids
  
  Optional Parameters:
  
  -MINLen=6                   Show all hits longer than 6 residues

LOCAL DATA FILES

The files described below supply auxiliary data to this program. The program automatically reads them from a public data directory unless you either 1) have a data file with exactly the same name in your current working directory; or 2) name a file on the command line with an expression like -DATa1=myfile.dat. For more information see Chapter 4, Using Data Files in the User's Guide.

File kolaskar.dat contains the values from the original paper. You can Fetch this file and edit the values.

Printed: April 22, 1996 15:52 (1162)