Limitations of homology searching for identification of T-cell antigens with library derived mimicry epitopes

Mimicry epitopes that are recognized by T-cells can be identified through s creening of synthetic peptide libraries. We have shown that these mimicry e pitopes share sequence similarity with the corresponding natural epitopes a nd that mimicry sequences can be used for the definition of protein derived T-cell epitopes from databases. This can be done by either homology search ing or pattern searching. Here we discuss the advantages and disadvantages of homology searching as an alternative for the generally applicable recogn ition pattern approach. We show that only for part of the library derived m imicry epitopes, the degree of similarity to the natural epitope may be hig h enough for successful homology searching in small databases, (C) 1999 Els evier Science Ltd. All rights reserved.