ArticleBioinformatics (Oxford, England)2019
OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers.
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138 citing papers in PubMed, 236 citations in OpenAlex.
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- The challenge and promise of studying human antigen-specific T cells.Nature reviews. Immunology · 2026Review
- DTCR: generating realistic, diverse, and epitope-specific T cell receptor sequences via a discrete diffusion model.Briefings in bioinformatics · 2026Article
- Diversity, Equality, and Inclusion in the naïve T Cell Receptor Repertoire.Immunological reviews · 2026Review
- Deciphering antigen-driven T cell responses through vectorized TCRdist sequence neighborhood quantification.bioRxiv : the preprint server for biology · 2026Article
- Large-scale paired chain BCR analysis reveals antibody clonal family inference bias and enhances resolution with machine learning.PLoS computational biology · 2026Article
- Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.Genome medicine · 2026Article
- DecoderTCR: Compositional Pretraining and Entropy-Guided Decoding for TCR-pMHC Interactions.bioRxiv : the preprint server for biology · 2026Article
- Systemic T Cell Receptor Profiling Reveals Adaptive Immune Activation and Potential Immune Signatures of Diagnosis and Brain Atrophy in Epilepsy.Annals of clinical and translational neurology · 2026Article
- The Abundance of α-Chain-Centric TCRs in the Mouse Repertoire of Primarily Activated Effectors and Reactivated Memory T Cells.Computational and structural biotechnology journal · 2026Article
- HLA alleles shape distinct biases in the usage preferences of TCR VFrontiers in immunology · 2026Article
- TCR repertoire shaping of naïve T cell subsets in human ontogeny.Frontiers in immunology · 2026Article
- Detecting statistical interactions in immune receptor data: a comparative study.Journal of applied statistics · 2026Article
- T Cell Receptor Sharing in Hypersensitivity Pneumonitis.Computational and structural biotechnology journal · 2026Article
- Immune signatures of common exposures through co-occurrence of T-cell receptors in tens of thousands of donors.Frontiers in immunology · 2026Article
78 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationHigh-throughput sequencing of large immune repertoires has enabled the development of methods to predict the probability of generation by V(D)J recombination of T- and B-cell receptors of any specific nucleotide sequence. These generation probabilities are very non-homogeneous, ranging over 20 orders of magnitude in real repertoires. Since the function of a receptor really depends on its protein sequence, it is important to be able to predict this probability of generation at the amino acid level. However, brute-force summation over all the nucleotide sequences with the correct amino acid translation is computationally intractable. The purpose of this paper is to present a solution to this problem.
resultsWe use dynamic programming to construct an efficient and flexible algorithm, called OLGA (Optimized Likelihood estimate of immunoGlobulin Amino-acid sequences), for calculating the probability of generating a given CDR3 amino acid sequence or motif, with or without V/J restriction, as a result of V(D)J recombination in B or T cells. We apply it to databases of epitope-specific T-cell receptors to evaluate the probability that a typical human subject will possess T cells responsive to specific disease-associated epitopes. The model prediction shows an excellent agreement with published data. We suggest that OLGA may be a useful tool to guide vaccine design. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/zsethna/OLGA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.