{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T23:11:43Z","timestamp":1771888303966,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2020,6,17]],"date-time":"2020-06-17T00:00:00Z","timestamp":1592352000000},"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\/100004807","name":"DFG","doi-asserted-by":"publisher","award":["SFB1310"],"award-info":[{"award-number":["SFB1310"]}],"id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004189","name":"Max Planck Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ERC CoG","award":["724208"],"award-info":[{"award-number":["724208"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Recent advances in modelling VDJ recombination and subsequent selection of T- and B-cell receptors provide useful tools to analyse and compare immune repertoires across time, individuals and tissues. A suite of tools\u2014IGoR, OLGA and SONIA\u2014have been publicly released to the community that allow for the inference of generative and selection models from high-throughput sequencing data. However, using these tools requires some scripting or command-line skills and familiarity with complex datasets. As a result, the application of the above models has not been available to a broad audience. In this application note, we fill this gap by presenting Simple OLGA &amp; SONIA (SOS), a web-based interface where users with no coding skills can compute the generation and post-selection probabilities of their sequences, as well as generate batches of synthetic sequences. The application also functions on mobile phones.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SOS is freely available to use at sites.google.com\/view\/statbiophysens\/sos with source code at github.com\/statbiophys\/sos.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa574","type":"journal-article","created":{"date-parts":[[2020,6,10]],"date-time":"2020-06-10T11:31:50Z","timestamp":1591788710000},"page":"4510-4512","source":"Crossref","is-referenced-by-count":6,"title":["SOS: online probability estimation and generation of T-and B-cell receptors"],"prefix":"10.1093","volume":"36","author":[{"given":"Giulio","family":"Isacchini","sequence":"first","affiliation":[{"name":"Laboratoire de physique de l\u2019\u00c9cole normale sup\u00e9rieure (PSL University), CNRS, Sorbonne Universit\u00e9, Universit\u00e9 de Paris , 75005 Paris, France"},{"name":"Max Planck Institute for Dynamics and Self-organization , 37077 G\u00f6ttingen, Germany"}]},{"given":"Carlos","family":"Olivares","sequence":"additional","affiliation":[{"name":"Laboratoire de physique de l\u2019\u00c9cole normale sup\u00e9rieure (PSL University), CNRS, Sorbonne Universit\u00e9, Universit\u00e9 de Paris , 75005 Paris, France"}]},{"given":"Armita","family":"Nourmohammad","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Dynamics and Self-organization , 37077 G\u00f6ttingen, Germany"},{"name":"Department of Physics, University of Washington , Seattle, WA 98195, USA"},{"name":"Fred Hutchinson Cancer Research Center , Seattle, WA 98109, USA"}]},{"given":"Aleksandra M","family":"Walczak","sequence":"additional","affiliation":[{"name":"Laboratoire de physique de l\u2019\u00c9cole normale sup\u00e9rieure (PSL University), CNRS, Sorbonne Universit\u00e9, Universit\u00e9 de Paris , 75005 Paris, France"}]},{"given":"Thierry","family":"Mora","sequence":"additional","affiliation":[{"name":"Laboratoire de physique de l\u2019\u00c9cole normale sup\u00e9rieure (PSL University), CNRS, Sorbonne Universit\u00e9, Universit\u00e9 de Paris , 75005 Paris, France"}]}],"member":"286","published-online":{"date-parts":[[2020,6,17]]},"reference":[{"key":"2023062213531125300_btaa574-B1","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1146\/annurev-immunol-042718-041757","article-title":"Using T cell receptor repertoires to understand the principles of adaptive immune recognition","volume":"37","author":"Bradley","year":"2019","journal-title":"Annu. 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Bioinf"},{"key":"2023062213531125300_btaa574-B5","author":"Isacchini","year":"2020"},{"key":"2023062213531125300_btaa574-B6","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1038\/s41467-018-02832-w","article-title":"High-throughput immune repertoire analysis with IGoR","volume":"9","author":"Marcou","year":"2018","journal-title":"Nat. Commun"},{"key":"2023062213531125300_btaa574-B7","author":"Minervina","year":"2019"},{"key":"2023062213531125300_btaa574-B8","doi-asserted-by":"crossref","first-page":"16161","DOI":"10.1073\/pnas.1212755109","article-title":"Statistical inference of the generation probability of T-cell receptors from sequence repertoires","volume":"109","author":"Murugan","year":"2012","journal-title":"Proc. Natl. Acad. Sci. 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Biol"},{"key":"2023062213531125300_btaa574-B10","doi-asserted-by":"crossref","first-page":"2974","DOI":"10.1093\/bioinformatics\/btz035","article-title":"OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs","volume":"35","author":"Sethna","year":"2019","journal-title":"Bioinformatics"},{"key":"2023062213531125300_btaa574-B11","first-page":"1","author":"Sethna","year":"2020"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa574\/33666275\/btaa574.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/16\/4510\/50677456\/btaa574.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/16\/4510\/50677456\/btaa574.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T20:50:44Z","timestamp":1687467044000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/16\/4510\/5858971"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,6,17]]},"references-count":11,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2020,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa574","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,8,15]]},"published":{"date-parts":[[2020,6,17]]}}}