{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T12:26:17Z","timestamp":1775478377395,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,9,11]],"date-time":"2016-09-11T00:00:00Z","timestamp":1473552000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"National Institute of Allergy and Infectious Diseases of the National Institutes of Health","award":["P01AI106697"],"award-info":[{"award-number":["P01AI106697"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["P30-CA016520"],"award-info":[{"award-number":["P30-CA016520"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>As high-throughput sequencing of B cells becomes more common, the need for tools to analyze the large quantity of data also increases. This article introduces ImmuneDB, a system for analyzing vast amounts of heavy chain variable region sequences and exploring the resulting data. It can take as input raw FASTA\/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>ImmuneDB is freely available at http:\/\/immunedb.com<\/jats:p>\n                  <jats:p>A demo of the ImmuneDB web interface is available at: http:\/\/immunedb.com\/demo<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw593","type":"journal-article","created":{"date-parts":[[2016,9,12]],"date-time":"2016-09-12T00:29:01Z","timestamp":1473640141000},"page":"292-293","source":"Crossref","is-referenced-by-count":29,"title":["ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data"],"prefix":"10.1093","volume":"33","author":[{"given":"Aaron M","family":"Rosenfeld","sequence":"first","affiliation":[{"name":"School of Biomedical Engineering Science and Health Systems, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenzhao","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eline T","family":"Luning Prak","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Uri","family":"Hershberg","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering Science and Health Systems, Drexel University, Philadelphia, PA, USA"},{"name":"Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,9,11]]},"reference":[{"key":"2023020204313135500_btw593-B1","first-page":"26","article-title":"Imgt\/highv-quest: The imgt web portal for immunoglobulin (IG) or antibody and t cell receptor (TR) analysis from NGS high throughput and deep sequencing","volume":"8","author":"Alamyar","year":"2012","journal-title":"Immunome Res"},{"key":"2023020204313135500_btw593-B2","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","article-title":"A general method applicable to the search for similarities in the amino acid sequence of two proteins","volume":"48","author":"Needleman","year":"1970","journal-title":"J. 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Biol"},{"key":"2023020204313135500_btw593-B3","doi-asserted-by":"crossref","first-page":"2823","DOI":"10.1093\/bioinformatics\/btl478","article-title":"Clearcut: a fast implementation of relaxed neighbor joining","volume":"22","author":"Sheneman","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020204313135500_btw593-B4","doi-asserted-by":"crossref","first-page":"1930","DOI":"10.1093\/bioinformatics\/btu138","article-title":"pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires","volume":"30","author":"Vander Heiden","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020204313135500_btw593-B5","doi-asserted-by":"crossref","first-page":"e134","DOI":"10.1093\/nar\/gks457","article-title":"Quantifying selection in high-throughput immunoglobulin sequencing data sets","volume":"40","author":"Yaari","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023020204313135500_btw593-B6","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.jim.2015.10.009","article-title":"Discrimination of germline v genes at different sequencing lengths and mutational burdens: a new tool for identifying and evaluating the reliability of v gene assignment","volume":"427","author":"Zhang","year":"2015","journal-title":"J. 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Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/2\/292\/49037502\/bioinformatics_33_2_292.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/2\/292\/49037502\/bioinformatics_33_2_292.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:33:18Z","timestamp":1675312398000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/2\/292\/2525702"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,9,11]]},"references-count":6,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2017,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw593","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,1,15]]},"published":{"date-parts":[[2016,9,11]]}}}