{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:47Z","timestamp":1740185147436,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2020,12,15]],"date-time":"2020-12-15T00:00:00Z","timestamp":1607990400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01 AI150739"],"award-info":[{"award-number":["U01 AI150739"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018183","name":"Human Vaccines Project","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100018183","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>B-cell receptor (BCR) and T-cell receptor (TCR) repertoires are generated through somatic DNA rearrangements and are responsible for the molecular basis of antigen recognition in the immune system. Next-generation sequencing (NGS) of DNA and the falling cost of sequencing due to continued development of these technologies have made sequencing assays an affordable way to characterize the repertoire of adaptive immune receptors (sometimes termed the \u2018immunome\u2019). Many new workflows have been developed to take advantage of NGS and have placed the resulting immunome datasets in the public domain. The scale of these NGS datasets has made it challenging to search through the Complementarity-determining region 3 (CDR3), which is responsible for imparting specific antibody-antigen interactions. Thus, there is an increasing demand for sequence analysis tools capable of searching through CDR3s from immunome data collections containing millions of sequences. To address this need, we created a software package called ClonoMatch that facilitates rapid searches in bulk immunome data for BCR or TCR sequences based on their CDR3 sequence or V3J clonotype.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Documentation, software support and the codebase are all available at https:\/\/github.com\/crowelab\/clonomatch. This software is distributed under the GPL v3 license.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1028","type":"journal-article","created":{"date-parts":[[2020,11,30]],"date-time":"2020-11-30T20:30:03Z","timestamp":1606768203000},"page":"5695-5697","source":"Crossref","is-referenced-by-count":2,"title":["ClonoMatch: a tool for identifying homologous immunoglobulin and T-cell receptor sequences in large databases"],"prefix":"10.1093","volume":"36","author":[{"given":"Taylor","family":"Jones","sequence":"first","affiliation":[{"name":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center , Nashville, TN 37232, USA"}]},{"given":"Samuel B","family":"Day","sequence":"additional","affiliation":[{"name":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center , Nashville, TN 37232, USA"}]},{"given":"Luke","family":"Myers","sequence":"additional","affiliation":[{"name":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center , Nashville, TN 37232, USA"}]},{"suffix":"Jr","given":"James E","family":"Crowe","sequence":"additional","affiliation":[{"name":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center , Nashville, TN 37232, USA"},{"name":"Department of Pediatrics, Vanderbilt University Medical Center , Nashville, TN 37232, USA"},{"name":"Department of Pathology, Microbiology, and Immunology, Vanderbilt University , Nashville, TN 37232, USA"}]},{"given":"Cinque","family":"Soto","sequence":"additional","affiliation":[{"name":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center , Nashville, TN 37232, USA"},{"name":"Department of Pediatrics, Vanderbilt University Medical Center , Nashville, TN 37232, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,12,16]]},"reference":[{"key":"2023062408140896100_btaa1028-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol"},{"key":"2023062408140896100_btaa1028-B2","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1038\/s41586-019-0879-y","article-title":"Commonality despite exceptional diversity in the baseline human antibody repertoire","volume":"566","author":"Briney","year":"2019","journal-title":"Nature"},{"key":"2023062408140896100_btaa1028-B3","doi-asserted-by":"crossref","first-page":"D67","DOI":"10.1093\/nar\/gkv1276","article-title":"GenBank","volume":"44","author":"Clark","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023062408140896100_btaa1028-B4","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1111\/imr.12666","article-title":"iReceptor: a platform for querying and analyzing antibody\/B-cell and T-cell receptor repertoire data across federated repositories","volume":"284","author":"Corrie","year":"2018","journal-title":"Immunol. 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