
doi: 10.1093/nar/gkx760
pmid: 28977646
pmc: PMC5753233
handle: 10029/621387 , 11343/222151 , 1959.4/unsworks_53122
doi: 10.1093/nar/gkx760
pmid: 28977646
pmc: PMC5753233
handle: 10029/621387 , 11343/222151 , 1959.4/unsworks_53122
The ability to decode antigen specificities encapsulated in the sequences of rearranged T-cell receptor (TCR) genes is critical for our understanding of the adaptive immune system and promises significant advances in the field of translational medicine. Recent developments in high-throughput sequencing methods (immune repertoire sequencing technology, or RepSeq) and single-cell RNA sequencing technology have allowed us to obtain huge numbers of TCR sequences from donor samples and link them to T-cell phenotypes. However, our ability to annotate these TCR sequences still lags behind, owing to the enormous diversity of the TCR repertoire and the scarcity of available data on T-cell specificities. In this paper, we present VDJdb, a database that stores and aggregates the results of published T-cell specificity assays and provides a universal platform that couples antigen specificities with TCR sequences. We demonstrate that VDJdb is a versatile instrument for the annotation of TCR repertoire data, enabling a concatenated view of antigen-specific TCR sequence motifs. VDJdb can be accessed at https://vdjdb.cdr3.net and https://github.com/antigenomics/vdjdb-db.
Models, Molecular, Secondary, T-Lymphocytes, Sequence Homology, Protein Structure, Secondary, Major Histocompatibility Complex, 3102 Bioinformatics and Computational Biology, Mice, Models, Receptors, Database Issue, anzsrc-for: 31 Biological Sciences, Databases, Protein, High-Throughput Nucleotide Sequencing, anzsrc-for: 41 Environmental sciences, Amino Acid, Antigen, anzsrc-for: 3102 Bioinformatics and Computational Biology, Single-Cell Analysis, Biotechnology, Protein Binding, Protein Structure, 570, Receptors, Antigen, T-Cell, 610, Databases, anzsrc-for: 34 Chemical sciences, Genetics, Animals, Humans, Protein Interaction Domains and Motifs, Amino Acid Sequence, Antigens, Internet, Binding Sites, Sequence Homology, Amino Acid, Protein, Molecular, anzsrc-for: 05 Environmental Sciences, Molecular Sequence Annotation, T-Cell, Macaca mulatta, anzsrc-for: 06 Biological Sciences, anzsrc-for: 08 Information and Computing Sciences, Sequence Alignment, Software, 31 Biological Sciences
Models, Molecular, Secondary, T-Lymphocytes, Sequence Homology, Protein Structure, Secondary, Major Histocompatibility Complex, 3102 Bioinformatics and Computational Biology, Mice, Models, Receptors, Database Issue, anzsrc-for: 31 Biological Sciences, Databases, Protein, High-Throughput Nucleotide Sequencing, anzsrc-for: 41 Environmental sciences, Amino Acid, Antigen, anzsrc-for: 3102 Bioinformatics and Computational Biology, Single-Cell Analysis, Biotechnology, Protein Binding, Protein Structure, 570, Receptors, Antigen, T-Cell, 610, Databases, anzsrc-for: 34 Chemical sciences, Genetics, Animals, Humans, Protein Interaction Domains and Motifs, Amino Acid Sequence, Antigens, Internet, Binding Sites, Sequence Homology, Amino Acid, Protein, Molecular, anzsrc-for: 05 Environmental Sciences, Molecular Sequence Annotation, T-Cell, Macaca mulatta, anzsrc-for: 06 Biological Sciences, anzsrc-for: 08 Information and Computing Sciences, Sequence Alignment, Software, 31 Biological Sciences
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