Calculation of Antigen Selection Pressure on Immunoglobulin Genes

Welcome to the website companion to the paper The Inference of Antigen Selection on Immunoglobulin Genes by Izidore Lossos et. al., which has appeared in the Journal of Immunology (2000, 165: 5133-5142).

The applet below simplifies the calculation of antigen selection pressure on immunoglobulin genes, by using the multinominal application model as is described in the manuscript by Izidore Lossos et. al.

The applet may be used as follows.

1. Copy and paste the FR sequence of the germline gene (including FR1, FR2 and FR3 segments) into the appropriate space designated FR. The sequence should consist of entries from the set T,G,A, C. Uppercase or lowercase is accepted and whitespace anywhere in the entire sequence is ignored, so you have some freedom in the input format. However, the total length of the sequence must be a multiple of 3.

   Please note that cutting and pasting from Microsoft Word programs to browsers can be problematic at times. The selection is usually copied, but the Paste menu is not highlighted. You can always copy with Control-c and paste with Control-v.

2. Copy and paste the CDR sequence of the germline gene (including CDR1, and CDR2 segments) into the appropriate space designed CDR. Again, as above, the sequence should consist of triples from the set T,G,A, C.
3. Fill in the number of replacement (R) and silent (S) mutations in the FR and CDR regions into the appropriate boxes. R1 denotes the replacement mutations in FR; S1, the silent mutations in FR; R2, the replacement mutations in CDR, and S2, the silent mutations in CDR.
4. Hit the Enter key on any of the R or S fields.

The applet then validates the input sequences and entries in various fields. If there is any error, it displays an error message. Otherwise, the resulting P-values for excess or scarcity of R mutations in the CDR and FR regions, respectively, will be calculated and displayed.