| URL: | https://vdjdb.cdr3.net |
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| Description: | VDJdb is a comprehensive database of antigen-specific T-cell receptor (TCR) sequences acquired by manual processing of published studies that report the ligand specificities of defined T-cell clonotypes (1). The primary goal of VDJdb is to facilitate access to existing information on TCR antigen specificities, i.e. the ability to recognize known epitopes presented by known major histocompatibility complex (MHC) class I and II molecules. |
| Year founded: | 2018 |
| Last update: | |
| Version: | |
| Accessibility: |
Manual:
Accessible
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| Country/Region: | Russian Federation |
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| Data object: |
NA
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| Database category: | |
| Major species: |
NA
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| Keywords: |
| University/Institution: | Pirogov Russian National Research Medical University |
| Address: | Pirogov Russian National Research Medical University, Moscow 117997, Russia Tel: +7 499 742 81 22; Fax: +7 495 330 70 56 |
| City: | |
| Province/State: | |
| Country/Region: | Russian Federation |
| Contact name (PI/Team): | Dmitriy M Chudakov |
| Contact email (PI/Helpdesk): | chudakovdm@mail.ru |
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VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium. [PMID: 31588507]
Here, we report an update of the VDJdb database with a substantial increase in the number of T-cell receptor (TCR) sequences and their cognate antigens. The update further provides a new database infrastructure featuring two additional analysis modes that facilitate database querying and real-world data analysis. The increased yield of TCR specificity identification methods and the overall increase in the number of studies in the field has allowed us to expand the database more than 5-fold. Furthermore, several new analysis methods are included. For example, batch annotation of TCR repertoire sequencing samples allows for annotating large datasets on-line. Using recently developed bioinformatic methods for TCR motif mining, we have built a reduced set of high-quality TCR motifs that can be used for both training TCR specificity predictors and matching against TCRs of interest. These additions enhance the versatility of the VDJdb in the task of exploring T-cell antigen specificities. The database is available at https://vdjdb.cdr3.net. |
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VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. [PMID: 28977646]
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. |