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TCR sequencing (TCR-Seq) technology has enabled accurate profiling TCR repertoire and currently a large number of TCR-Seq data are available in public. Based on the urgent need to effectively re-use these data, we developed TCRdb, a comprehensive human TCR sequences database, by a uniform pipeline to characterize TCR sequences on TCR-Seq data. TCRdb contains more than 277 million highly reliable TCR sequences from over 8265\u00a0TCR-Seq samples across hundreds of tissues\/clinical conditions\/cell types. The unique features of TCRdb include: (i) comprehensive and reliable sequences for TCR repertoire in different samples generated by a strict and uniform pipeline of TCRdb; (ii) powerful search function, allowing users to identify their interested TCR sequences in different conditions; (iii) categorized sample metadata, enabling comparison of TCRs in different sample types; (iv) interactive data visualization charts, describing the TCR repertoire in TCR diversity, length distribution and V-J gene utilization. The TCRdb database is freely available at http:\/\/bioinfo.life.hust.edu.cn\/TCRdb\/ and will be a useful resource in the research and application community of T cell immunology.<\/jats:p>","DOI":"10.1093\/nar\/gkaa796","type":"journal-article","created":{"date-parts":[[2020,9,11]],"date-time":"2020-09-11T11:12:29Z","timestamp":1599822749000},"page":"D468-D474","source":"Crossref","is-referenced-by-count":99,"title":["TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8076-0576","authenticated-orcid":false,"given":"Si-Yi","family":"Chen","sequence":"first","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China"}]},{"given":"Tao","family":"Yue","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China"}]},{"given":"Qian","family":"Lei","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5099-7465","authenticated-orcid":false,"given":"An-Yuan","family":"Guo","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China"}]}],"member":"286","published-online":{"date-parts":[[2020,9,29]]},"reference":[{"key":"2021010313132970200_B1","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/S0952-7915(97)80152-5","article-title":"Innate immunity: impact on the adaptive immune response","volume":"9","author":"Medzhitov","year":"1997","journal-title":"Curr. Opin. Immunol."},{"key":"2021010313132970200_B2","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/S0092-8674(04)00039-X","article-title":"Unraveling V(D)J recombination; insights into gene regulation","volume":"116","author":"Jung","year":"2004","journal-title":"Cell"},{"key":"2021010313132970200_B3","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1038\/334395a0","article-title":"T-cell antigen receptor genes and T-cell recognition","volume":"334","author":"Davis","year":"1988","journal-title":"Nature"},{"key":"2021010313132970200_B4","doi-asserted-by":"crossref","first-page":"aar5894","DOI":"10.1126\/scitranslmed.aar5894","article-title":"High-throughput sequencing of the T cell receptor \u03b2 gene identifies aggressive early-stage mycosis fungoides","volume":"10","author":"de\u00a0Masson","year":"2018","journal-title":"Sci. Transl. 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