ArticleBriefings in bioinformatics2024
tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- T-cell receptor repertoires against HLA class I-restricted minor histocompatibility antigens are highly diverse with a small subset of public clonotypes.Journal for immunotherapy of cancer · 2026Article
- Genome-wide characterization of the bZIP gene family in Rattus norvegicus and expression profiling analysis during brain development.BMC genomics · 2026Article
- Deciphering antigen-driven T cell responses through vectorized TCRdist sequence neighborhood quantification.bioRxiv : the preprint server for biology · 2026Article
- Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification.PLoS computational biology · 2026Article
- Machine learning in AIRR diagnostics: Advances and applications.Immunoinformatics (Amsterdam, Netherlands) · 2025Article
- Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires.Nucleic acids research · 2025Article
- SageTCR: a structure-based model integrating residue- and atom-level representations for enhanced TCR-pMHC binding prediction.Briefings in bioinformatics · 2025Article
- Computation strategies and clinical applications in neoantigen discovery towards precision cancer immunotherapy.Biomarker research · 2025Review
- Assessing the generalization capabilities of TCR binding predictors via peptide distance analysis.PloS one · 2025Article
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Authors and funding
4 authors.
Funding
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 substitution matrices for CDR3 alpha and CDR3 beta TCR chains, respectively. The matrices reflect AA frequencies and variations occurring within TCRs that bind the same epitope, revealing that both CDR3 alpha and CDR3 beta display tolerance to a wide range of AA substitutions and differ noticeably from the standard BLOSUM62. By accurately aligning distant TCRs employing tcrBLOSUMb, we were able to improve clustering performance and capture a large number of epitope-specific TCRs with diverse AA compositions and physicochemical profiles overlooked by BLOSUM62. Utilizing both the general BLOSUM62 and specialized tcrBLOSUM matrices in existing computational tools will broaden the range of TCRs that can be associated with their cognate epitopes, thereby enhancing TCR repertoire analysis.
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