We are trying to use computational methods to select peptides that
are likely to be specific in T cell proliferation assays, with the
ultimate aim of using them as specific reagents in a skin test for
leprosy. We have just finished selecting peptides from leprae proteins
from the SwissProt bank, and have the feeling there must be an easier way
of doing the computer work! I'll describe what we did and would be
grateful for any suggestion as to ways it could be made easier. Does
anyone now of any software that would be suitable?
I made a profile for use with MAP that contained 5 different DR motifs
constructed according to a review on the sequences of peptides eluted from
HLA molecules. This was used to search the 68 leprae proteins in
SwissProt. Results were first printed out with MAPPLOT, and checked
visually for protein with short regions that contained at least 3 motifs.
Results from proteins meeting these criteria were then printed using MAP
so that the peptide sequence could be inspected.
A total of 202 (!) 15-mer peptides were subsequently selected that
contained at least 3 of the motifs. All 202 were then used in a TFASTA
search against GenEMBL to check for leprae specificity. We looked at the
hits from the TFASTA search for each peptide and if any shared 10 or or
more residues with the peptide then that peptides was discarded as
potentially compromising specificity. This left 140 peptides, which will
now be synthesised and tested in pools for T-cell proliferation.
We had originally intended to use the cosmid sequences from the leprae
genome project, where there are about 200 ORFs with no known homologs.
However having got 202 initial peptides from only 68 proteins we have
decided against this for the time being, until there are other programs
available which would streamline the procedure - it was very tedious to do
by hand !!
Any suggestions please let me know, either directly or via the list.
Dr. Brian D. Robertson
Dept. Medical Microbiology
St Mary's Hospital Medical School
London W2 1PG
b.robertson at sm.ic.ac.uk