Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires.

ABSTRACT: A continued challenge in the analysis of adaptive immune receptor repertoires (AIRRs) is the prediction of antigen reactivity from primary sequence data. Many algorithms infer antigen-specific responses by measuring sequence similarity between receptors. Similarity is often scored using tools for protein alignment such as the BLOSUM matrices. However, these metrics were designed to identify homology in genomic proteins, not VDJ-recombined immune receptors. Comparison of these metrics against other approaches is underexplored. We used matrix factorization to make physiochemical-based alternatives which may improve performance. We evaluated these metrics by clustering 383 simulated and biological repertoires using traditional and physiochemical-based scoring matrices. While physiochemical an

SUBMITTER: Girgis AA 

PROVIDER: S-EPMC12630133 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature