TcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs.

ABSTRACT: Deciphering the specificity of T-cell receptor (TCR) repertoires is crucial for monitoring adaptive immune responses and developing targeted immunotherapies and vaccines. To elucidate the specificity of previously unseen TCRs, many methods employ the BLOSUM62 matrix to find TCRs with similar amino acid (AA) sequences. However, while BLOSUM62 reflects the AA substitutions within conserved regions of proteins with similar functions, the remarkable diversity of TCRs means that both TCRs with similar and dissimilar sequences can bind the same epitope. Therefore, reliance on BLOSUM62 may bias detection towards epitope-specific TCRs with similar biochemical properties, overlooking those with more diverse AA compositions. In this study, we introduce tcrBLOSUMa and tcrBLOSUMb, specialized AA subst

SUBMITTER: Postovskaya A 

PROVIDER: S-EPMC11583439 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature