{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T01:24:23Z","timestamp":1780363463757,"version":"3.54.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,3]],"date-time":"2024-12-03T00:00:00Z","timestamp":1733184000000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Antibodies are a cornerstone of the immune system, playing a pivotal role in identifying and neutralizing infections caused by bacteria, viruses, and other pathogens. Understanding their structure, and function, can provide insights into both the body\u2019s natural defenses and the principles behind many therapeutic interventions, including vaccines and antibody-based drugs. The analysis and annotation of antibody sequences, including the identification of variable, diversity, joining, and constant genes, as well as the delineation of framework regions and complementarity-determining regions, is essential for understanding their structure and function. Currently analyzing large volumes of antibody sequences is routine in antibody discovery, requiring fast and accurate tools. While there are existing tools designed for the annotation and numbering of antibody sequences, they often have limitations such as being restricted to either nucleotide or amino acid sequences; slow execution times; or reliance on germline databases that are closed, frequently changed, or have sparse coverage for some species. Here, we present the Rapid Immunoglobulin Overview Tool (RIOT), a novel open-source solution for antibody numbering that addresses these shortcomings. RIOT handles nucleotide and amino acid sequence processing, comes integrated with an Open Germline Receptor Database, and is computationally efficient. We hope that the tool will facilitate rapid annotation of antibody sequencing outputs for the benefit of understanding antibody biology and discovering novel therapeutics.<\/jats:p>","DOI":"10.1093\/bib\/bbae632","type":"journal-article","created":{"date-parts":[[2024,12,14]],"date-time":"2024-12-14T11:09:47Z","timestamp":1734174587000},"source":"Crossref","is-referenced-by-count":11,"title":["RIOT\u2014Rapid Immunoglobulin Overview Tool\u2014annotation of nucleotide and amino acid immunoglobulin sequences using an open germline database"],"prefix":"10.1093","volume":"26","author":[{"given":"Pawe\u0142","family":"Dudzic","sequence":"first","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bartosz","family":"Janusz","sequence":"additional","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tadeusz","family":"Sat\u0142awa","sequence":"additional","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dawid","family":"Chomicz","sequence":"additional","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomasz","family":"Gaw\u0142owski","sequence":"additional","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafa\u0142","family":"Grabowski","sequence":"additional","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Przemek","family":"J\u00f3\u017awiak","sequence":"additional","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mateusz","family":"Tarkowski","sequence":"additional","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maciej","family":"Mycielski","sequence":"additional","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonia","family":"Wr\u00f3bel","sequence":"additional","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0697-5522","authenticated-orcid":false,"given":"Konrad","family":"Krawczyk","sequence":"additional","affiliation":[{"name":"NaturalAntibody S.A. , Al. Piast\u00f3w 22, 71-064 Szczecin ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,12,2]]},"reference":[{"key":"2024121411093953900_ref1","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1111\/imm.13176","article-title":"V(D)J recombination, somatic hypermutation and class switch recombination of immunoglobulins: mechanism and regulation","volume":"160","author":"Chi","year":"2020","journal-title":"Immunology"},{"key":"2024121411093953900_ref2","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1146\/annurev.immunol.14.1.441","article-title":"Somatic hypermutation of immunoglobulin genes","volume":"14","author":"Wagner","year":"1996","journal-title":"Annu Rev Immunol"},{"key":"2024121411093953900_ref3","doi-asserted-by":"publisher","first-page":"2297450","DOI":"10.1080\/19420862.2023.2297450","article-title":"Antibodies to watch in 2024","volume":"16","author":"Crescioli","year":"2024","journal-title":"MAbs"},{"key":"2024121411093953900_ref4"},{"key":"2024121411093953900_ref5","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1006\/jmbi.1997.1354","article-title":"Standard conformations for the canonical structures of immunoglobulins","volume":"273","author":"Al-Lazikani","year":"1997","journal-title":"J Mol Biol"},{"key":"2024121411093953900_ref6","doi-asserted-by":"publisher","first-page":"3832","DOI":"10.1016\/j.molimm.2008.05.022","article-title":"Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains","volume":"45","author":"Abhinandan","year":"2008","journal-title":"Mol Immunol"},{"key":"2024121411093953900_ref7","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/S0145-305X(02)00039-3","article-title":"IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains","volume":"27","author":"Lefranc","year":"2003","journal-title":"Dev Comp Immunol"},{"key":"2024121411093953900_ref8","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1006\/jmbi.2001.4662","article-title":"Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool","volume":"309","author":"Honegger","year":"2001","journal-title":"J Mol Biol"},{"key":"2024121411093953900_ref9","doi-asserted-by":"publisher","first-page":"71","DOI":"10.3233\/HAB-230014","article-title":"Significance of antibody numbering systems in the development of antibody engineering","volume":"31","author":"Patel","year":"2023","journal-title":"Hum Antibodies"},{"key":"2024121411093953900_ref10","doi-asserted-by":"publisher","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"2024121411093953900_ref11","doi-asserted-by":"publisher","first-page":"W34","DOI":"10.1093\/nar\/gkt382","article-title":"IgBLAST: an immunoglobulin variable domain sequence analysis tool","volume":"41","author":"Ye","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2024121411093953900_ref12","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1093\/bioinformatics\/btv552","article-title":"ANARCI: antigen receptor numbering and receptor classification","volume":"32","author":"Dunbar","year":"2016","journal-title":"Bioinformatics"},{"key":"2024121411093953900_ref13","doi-asserted-by":"publisher","first-page":"1524","DOI":"10.1002\/pro.3633","article-title":"AbRSA: a robust tool for antibody numbering","volume":"28","author":"Li","year":"2019","journal-title":"Protein Sci"},{"key":"2024121411093953900_ref14","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1016\/j.jmb.2016.08.019","article-title":"abYsis: integrated antibody sequence and structure-management, analysis, and prediction","volume":"429","author":"Swindells","year":"2017","journal-title":"J Mol Biol"},{"key":"2024121411093953900_ref15","doi-asserted-by":"publisher","first-page":"btae278","DOI":"10.1093\/bioinformatics\/btae278","article-title":"For antibody sequence generative modeling, mixture models may be all you need","volume":"40","author":"Parkinson","year":"2024","journal-title":"Bioinformatics"},{"key":"2024121411093953900_ref16","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1093\/nar\/gkg085","article-title":"IMGT, the international ImMunoGeneTics database","volume":"31","author":"Lefranc","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2024121411093953900_ref17","doi-asserted-by":"publisher","first-page":"D964","DOI":"10.1093\/nar\/gkz822","article-title":"OGRDB: a reference database of inferred immune receptor genes","volume":"48","author":"Lees","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024121411093953900_ref18","doi-asserted-by":"publisher","first-page":"100025","DOI":"10.1016\/j.immuno.2023.100025","article-title":"AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets","volume":"10","author":"Lees","year":"2023","journal-title":"Immunoinformatics (Amst)"},{"key":"2024121411093953900_ref19","doi-asserted-by":"publisher","first-page":"D1051","DOI":"10.1093\/nar\/gkz872","article-title":"VDJbase: an adaptive immune receptor genotype and haplotype database","volume":"48","author":"Omer","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024121411093953900_ref20","doi-asserted-by":"publisher","first-page":"1731","DOI":"10.1093\/bioinformatics\/btz845","article-title":"Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences","volume":"36","author":"Smakaj","year":"2020","journal-title":"Bioinformatics"},{"key":"2024121411093953900_ref21","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1093\/bioinformatics\/btl582","article-title":"Striped Smith-Waterman speeds database searches six times over other SIMD implementations","volume":"23","author":"Farrar","year":"2007","journal-title":"Bioinformatics"},{"key":"2024121411093953900_ref22","doi-asserted-by":"publisher","first-page":"1892366","DOI":"10.1080\/19420862.2021.1892366","article-title":"Data mining patented antibody sequences","volume":"13","author":"Krawczyk","year":"2021","journal-title":"MAbs"},{"key":"2024121411093953900_ref23"},{"key":"2024121411093953900_ref24","doi-asserted-by":"publisher","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":"2024121411093953900_ref25","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2024121411093953900_ref26","doi-asserted-by":"publisher","first-page":"588","DOI":"10.1038\/s41592-021-01169-5","article-title":"Diversity in immunogenomics: the value and the challenge","volume":"18","author":"Peng","year":"2021","journal-title":"Nat Methods"},{"key":"2024121411093953900_ref27","doi-asserted-by":"publisher","first-page":"D54","DOI":"10.1093\/nar\/gki031","article-title":"Entrez gene: gene-centered information at NCBI","volume":"33","author":"Maglott","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2024121411093953900_ref28","doi-asserted-by":"publisher","first-page":"2361928","DOI":"10.1080\/19420862.2024.2361928","article-title":"Large-scale data mining of four billion human antibody variable regions reveals convergence between therapeutic and natural antibodies that constrains search space for biologics drug discovery","volume":"16","author":"Dudzic","year":"2024","journal-title":"MAbs"},{"key":"2024121411093953900_ref29","doi-asserted-by":"publisher","first-page":"2628","DOI":"10.1093\/bioinformatics\/btac151","article-title":"AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design","volume":"38","author":"M\u0142okosiewicz","year":"2022","journal-title":"Bioinformatics"},{"key":"2024121411093953900_ref30","doi-asserted-by":"publisher","first-page":"11","DOI":"10.3389\/fmolb.2024.1352508","article-title":"Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications","volume":"11","author":"Chomicz","year":"2024","journal-title":"Front Mol Biosci"},{"key":"2024121411093953900_ref31","doi-asserted-by":"publisher","first-page":"i341","DOI":"10.1093\/bioinformatics\/bty235","article-title":"A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data","volume":"34","author":"Nouri","year":"2018","journal-title":"Bioinformatics"},{"key":"2024121411093953900_ref32","doi-asserted-by":"publisher","first-page":"1330153","DOI":"10.3389\/fimmu.2023.1330153","article-title":"AIRR-C IG reference sets: curated sets of immunoglobulin heavy and light chain germline genes","volume":"14","author":"Collins","year":"2023","journal-title":"Front Immunol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/1\/bbae632\/60929561\/bbae632.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/1\/bbae632\/60929561\/bbae632.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,14]],"date-time":"2024-12-14T11:09:49Z","timestamp":1734174589000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae632\/7914577"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,22]]},"references-count":32,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,11,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae632","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2024,11,22]]},"article-number":"bbae632"}}