{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:10:58Z","timestamp":1772165458553,"version":"3.50.1"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,10,8]],"date-time":"2020-10-08T00:00:00Z","timestamp":1602115200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,10,8]],"date-time":"2020-10-08T00:00:00Z","timestamp":1602115200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Repertoire analysis of patient-derived recombinant monoclonal antibodies is an important tool to study the role of B cells in autoimmune diseases of the human brain and beyond. Current protocols for generation of patient-derived recombinant monoclonal antibody libraries are time-consuming and contain repetitive steps, some of which can be assisted with the help of software automation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed BASE, an easy-to-use software for complete data analysis in single cell immunoglobulin cloning. BASE consists of two modules: aBASE for immunological annotations and cloning primer lookup, and cBASE for plasmid sequence identity confirmation before expression. Comparing automated BASE analysis with manual analysis we confirmed the validity of BASE output: identity between manual and automated aBASE analysis was 100% for all outputs, except for immunoglobulin isotype determination. In this case, aBASE yielded correct results in 96% of cases, whereas 4% of cases required manual confirmation. cBASE automatically concluded expression recommendations in 89.8% of cases, 91.8% of which were identical to manually derived results and none of them were false-positive.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>BASE offers an easy-to-use software solution suitable for complete Ig sequence data analysis and tracking during recombinant mAb cloning from single cells. Plasmid sequence identity confirmation by cBASE offers functionality not provided by existing software solutions in the field and will help to reduce time-consuming steps of the monoclonal antibody generation workflow. BASE can be installed locally or accessed online at Code Ocean.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-020-03741-w","type":"journal-article","created":{"date-parts":[[2020,10,8]],"date-time":"2020-10-08T07:02:48Z","timestamp":1602140568000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Brain antibody sequence evaluation (BASE): an easy-to-use software for complete data analysis in single cell immunoglobulin cloning"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8132-3527","authenticated-orcid":false,"given":"S. Momsen","family":"Reincke","sequence":"first","affiliation":[]},{"given":"Harald","family":"Pr\u00fcss","sequence":"additional","affiliation":[]},{"given":"Jakob","family":"Kreye","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,10,8]]},"reference":[{"issue":"5638","key":"3741_CR1","doi-asserted-by":"publisher","first-page":"1374","DOI":"10.1126\/science.1086907","volume":"301","author":"H Wardemann","year":"2003","unstructured":"Wardemann H, et al. Predominant autoantibody production by early human B cell precursors. Science. 2003;301(5638):1374\u20137.","journal-title":"Science"},{"issue":"7238","key":"3741_CR2","doi-asserted-by":"publisher","first-page":"636","DOI":"10.1038\/nature07930","volume":"458","author":"JF Scheid","year":"2009","unstructured":"Scheid JF, et al. Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals. Nature. 2009;458(7238):636\u201340.","journal-title":"Nature"},{"issue":"7","key":"3741_CR3","doi-asserted-by":"publisher","first-page":"1991","DOI":"10.1084\/jem.20160201","volume":"214","author":"JN Schickel","year":"2017","unstructured":"Schickel JN, et al. Self-reactive VH4-34-expressing IgG B cells recognize commensal bacteria. J Exp Med. 2017;214(7):1991\u20132003.","journal-title":"J Exp Med"},{"issue":"5","key":"3741_CR4","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1002\/ana.21802","volume":"66","author":"JL Bennett","year":"2009","unstructured":"Bennett JL, et al. Intrathecal pathogenic anti-aquaporin-4 antibodies in early neuromyelitis optica. Ann Neurol. 2009;66(5):617\u201329.","journal-title":"Ann Neurol"},{"issue":"Pt 10","key":"3741_CR5","doi-asserted-by":"publisher","first-page":"2641","DOI":"10.1093\/brain\/aww208","volume":"139","author":"J Kreye","year":"2016","unstructured":"Kreye J, et al. Human cerebrospinal fluid monoclonal N-methyl-D-aspartate receptor autoantibodies are sufficient for encephalitis pathogenesis. Brain. 2016;139(Pt 10):2641\u201352.","journal-title":"Brain"},{"issue":"11","key":"3741_CR6","doi-asserted-by":"publisher","first-page":"768","DOI":"10.1002\/acn3.444","volume":"4","author":"M Malviya","year":"2017","unstructured":"Malviya M, et al. NMDAR encephalitis: passive transfer from man to mouse by a recombinant antibody. Ann Clin Transl Neurol. 2017;4(11):768\u201383.","journal-title":"Ann Clin Transl Neurol"},{"issue":"5","key":"3741_CR7","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1002\/ana.25552","volume":"86","author":"B Jurek","year":"2019","unstructured":"Jurek B, et al. Human gestational NMDAR autoantibodies impair neonatal murine brain function. Ann Neurol. 2019;86(5):656\u201370.","journal-title":"Ann Neurol"},{"issue":"11","key":"3741_CR8","doi-asserted-by":"publisher","first-page":"2625","DOI":"10.1007\/s00415-018-9042-1","volume":"265","author":"LT Ly","year":"2018","unstructured":"Ly LT, et al. Affinities of human NMDA receptor autoantibodies: implications for disease mechanisms and clinical diagnostics. J Neurol. 2018;265(11):2625\u201332.","journal-title":"J Neurol"},{"issue":"3","key":"3741_CR9","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1002\/ana.22657","volume":"71","author":"L Tradtrantip","year":"2012","unstructured":"Tradtrantip L, et al. Anti-Aquaporin-4 monoclonal antibody blocker therapy for neuromyelitis optica. Ann Neurol. 2012;71(3):314\u201322.","journal-title":"Ann Neurol"},{"key":"3741_CR10","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1186\/s12865-014-0059-7","volume":"15","author":"MJ Moorhouse","year":"2014","unstructured":"Moorhouse MJ, et al. ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS. BMC Immunol. 2014;15:59.","journal-title":"BMC Immunol"},{"issue":"13","key":"3741_CR11","doi-asserted-by":"publisher","first-page":"1930","DOI":"10.1093\/bioinformatics\/btu138","volume":"30","author":"JA Vander Heiden","year":"2014","unstructured":"Vander Heiden JA, et al. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. 2014;30(13):1930\u20132.","journal-title":"Bioinformatics"},{"issue":"20","key":"3741_CR12","doi-asserted-by":"publisher","first-page":"3356","DOI":"10.1093\/bioinformatics\/btv359","volume":"31","author":"NT Gupta","year":"2015","unstructured":"Gupta NT, et al. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics. 2015;31(20):3356\u20138.","journal-title":"Bioinformatics"},{"key":"3741_CR13","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1186\/s12859-016-0920-1","volume":"17","author":"K Imkeller","year":"2016","unstructured":"Imkeller K, et al. sciReptor: analysis of single-cell level immunoglobulin repertoires. BMC Bioinformatics. 2016;17:67.","journal-title":"BMC Bioinformatics"},{"issue":"Web Server issu","key":"3741_CR14","doi-asserted-by":"publisher","first-page":"W34","DOI":"10.1093\/nar\/gkt382","volume":"41","author":"J Ye","year":"2013","unstructured":"Ye J, et al. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 2013;41(Web Server issue):W34\u201340.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"3741_CR15","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, et al. Basic local alignment search tool. J Mol Biol. 1990;215(3):403\u201310.","journal-title":"J Mol Biol"},{"key":"3741_CR16","doi-asserted-by":"publisher","unstructured":"Brain Antibody Sequence Evaluation (BASE). https:\/\/codeocean.com\/capsule\/9813295\/tree\/v1. https:\/\/doi.org\/10.24433\/CO.3514767.v1.","DOI":"10.24433\/CO.3514767.v1"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-03741-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-020-03741-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-03741-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,7]],"date-time":"2021-10-07T19:37:59Z","timestamp":1633635479000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-020-03741-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,10,8]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["3741"],"URL":"https:\/\/doi.org\/10.1186\/s12859-020-03741-w","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/836999","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,10,8]]},"assertion":[{"value":"13 November 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 September 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 October 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"446"}}