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
The applet may be used as follows.
- 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.
- 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.
- 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
- Hit the Enter key on any of the R or
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.
In case of problems, please email us with a description of your problem,
along with the inputs you used.
Last modified: Thu Dec 16 13:43:06 PST 1999