{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T09:13:19Z","timestamp":1792141999443,"version":"4.4.0"},"reference-count":68,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,19]],"date-time":"2023-05-19T00:00:00Z","timestamp":1684454400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81973243, 32000472"],"award-info":[{"award-number":["81973243, 32000472"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["KFJ-BRP-008"],"award-info":[{"award-number":["KFJ-BRP-008"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NHC and Shanghai Key Labs SIBPT","award":["RC2023-01"],"award-info":[{"award-number":["RC2023-01"]}]},{"name":"Shanghai Academy of Science&Technology","award":["SKY2022003"],"award-info":[{"award-number":["SKY2022003"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The utilization of high-throughput sequencing (HTS) for B-cell receptor (BCR) immune repertoire analysis has become widespread in the fields of adaptive immunity and antibody drug development. However, the sheer volume of sequences generated by these experiments presents a challenge in data processing. Specifically, multiple sequence alignment (MSA), a critical aspect of BCR analysis, remains inadequate for handling massive BCR sequencing data and lacks the ability to provide immunoglobulin-specific information. To address this gap, we introduce Abalign, a standalone program specifically designed for ultrafast MSA of BCR\/antibody sequences. Benchmark tests demonstrate that Abalign achieves comparable or even better accuracy than state-of-the-art MSA tools, and shows remarkable advantages in terms of speed and memory consumption, reducing the time required for high-throughput analysis from weeks to hours. In addition to its alignment capabilities, Abalign offers a broad range of BCR analysis features, including extracting BCRs, constructing lineage trees, assigning VJ genes, analyzing clonotypes, profiling mutations, and comparing BCR immune repertoires. With its user-friendly graphic interface, Abalign can be easily run on personal computers instead of computing clusters. Overall, Abalign is an easy-to-use and effective tool that enables researchers to analyze massive BCR\/antibody sequences, leading to new discoveries in the field of immunoinformatics. The software is freely available at http:\/\/cao.labshare.cn\/abalign\/.<\/jats:p>","DOI":"10.1093\/nar\/gkad400","type":"journal-article","created":{"date-parts":[[2023,5,19]],"date-time":"2023-05-19T20:22:21Z","timestamp":1684527741000},"page":"W17-W24","source":"Crossref","is-referenced-by-count":23,"title":["Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires"],"prefix":"10.1093","volume":"51","author":[{"given":"Fanjie","family":"Zong","sequence":"first","affiliation":[{"name":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , China"},{"name":"Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province , Chengdu , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenyu","family":"Long","sequence":"additional","affiliation":[{"name":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , China"},{"name":"Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province , Chengdu , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanxin","family":"Hu","sequence":"additional","affiliation":[{"name":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , China"},{"name":"Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province , Chengdu , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuang","family":"Chen","sequence":"additional","affiliation":[{"name":"Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wentao","family":"Dai","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Reproduction Regulation & Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies , Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi-Xiong","family":"Xiao","sequence":"additional","affiliation":[{"name":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1925-2123","authenticated-orcid":false,"given":"Yang","family":"Cao","sequence":"additional","affiliation":[{"name":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , China"},{"name":"Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province , Chengdu , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,19]]},"reference":[{"key":"2023070504575684400_B1","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1016\/0092-8674(81)90399-8","article-title":"Antibody diversity: somatic hypermutation of rearranged VH genes","volume":"27","author":"Kim","year":"1981","journal-title":"Cell"},{"key":"2023070504575684400_B2","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/302575a0","article-title":"Somatic generation of antibody diversity","volume":"302","author":"Tonegawa","year":"1983","journal-title":"Nature"},{"key":"2023070504575684400_B3","first-page":"MDNA3-0037\u20132014","article-title":"Related mechanisms of antibody somatic hypermutation and class switch recombination","volume":"3","author":"Hwang","year":"2015","journal-title":"Microbiol. Spectr."},{"key":"2023070504575684400_B4","doi-asserted-by":"crossref","first-page":"2203","DOI":"10.1172\/JCI78083","article-title":"Checkpoints that control B cell development","volume":"125","author":"Melchers","year":"2015","journal-title":"J. Clin. Invest."},{"key":"2023070504575684400_B5","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/s41435-021-00145-5","article-title":"Immunoglobulin germline gene variation and its impact on human disease","volume":"22","author":"Mikocziova","year":"2021","journal-title":"Genes Immun."},{"key":"2023070504575684400_B6","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/gene.2016.9","article-title":"Current status and recent advances of next generation sequencing techniques in immunological repertoire","volume":"17","author":"Hou","year":"2016","journal-title":"Genes and immunity"},{"key":"2023070504575684400_B7","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.coisb.2016.12.009","article-title":"Advances and applications of immune receptor sequencing in systems immunology","volume":"1","author":"Lindau","year":"2017","journal-title":"Current Opinion in Systems Biology"},{"key":"2023070504575684400_B8","doi-asserted-by":"crossref","first-page":"788","DOI":"10.1158\/2326-6066.CIR-21-0965","article-title":"Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies","volume":"10","author":"Song","year":"2022","journal-title":"Cancer Immunol. Res."},{"key":"2023070504575684400_B9","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/s10038-017-0364-0","article-title":"Characterization of the B-cell receptor repertoires in peanut allergic subjects undergoing oral immunotherapy","volume":"63","author":"Kiyotani","year":"2018","journal-title":"J. Hum. Genet."},{"key":"2023070504575684400_B10","doi-asserted-by":"crossref","first-page":"9823","DOI":"10.1074\/jbc.REV120.010181","article-title":"How repertoire data are changing antibody science","volume":"295","author":"Marks","year":"2020","journal-title":"J. Biol. Chem."},{"key":"2023070504575684400_B11","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/s13073-015-0243-2","article-title":"Practical guidelines for B-cell receptor repertoire sequencing analysis","volume":"7","author":"Yaari","year":"2015","journal-title":"Genome Med."},{"key":"2023070504575684400_B12","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/s41592-021-01142-2","article-title":"TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data","volume":"18","author":"Song","year":"2021","journal-title":"Nat. Methods"},{"key":"2023070504575684400_B13","doi-asserted-by":"crossref","first-page":"4255","DOI":"10.1093\/bioinformatics\/btaa432","article-title":"An ultra-sensitive T-cell receptor detection method for TCR-seq and RNA-seq data","volume":"36","author":"Chen","year":"2020","journal-title":"Bioinformatics"},{"key":"2023070504575684400_B14","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/nmeth.3364","article-title":"MiXCR: software for comprehensive adaptive immunity profiling","volume":"12","author":"Bolotin","year":"2015","journal-title":"Nat. Methods"},{"key":"2023070504575684400_B15","doi-asserted-by":"crossref","first-page":"3369","DOI":"10.4049\/jimmunol.1700485","article-title":"Reconstructing antibody repertoires from error-prone immunosequencing reads","volume":"199","author":"Shlemov","year":"2017","journal-title":"J. Immunol."},{"key":"2023070504575684400_B16","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\u00a0Heiden","year":"2014","journal-title":"Bioinformatics"},{"key":"2023070504575684400_B17","doi-asserted-by":"crossref","first-page":"2963","DOI":"10.1093\/bioinformatics\/btv309","article-title":"IMSEQ\u2014a fast and error aware approach to immunogenetic sequence analysis","volume":"31","author":"Kuchenbecker","year":"2015","journal-title":"Bioinformatics"},{"key":"2023070504575684400_B18","doi-asserted-by":"crossref","first-page":"3356","DOI":"10.1093\/bioinformatics\/btv359","article-title":"Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data","volume":"31","author":"Gupta","year":"2015","journal-title":"Bioinformatics"},{"key":"2023070504575684400_B19","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.jim.2008.06.006","article-title":"IgTree: creating immunoglobulin variable region gene lineage trees","volume":"338","author":"Barak","year":"2008","journal-title":"J. Immunol. Methods"},{"key":"2023070504575684400_B20","doi-asserted-by":"crossref","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":"2023070504575684400_B21","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1007\/978-1-61779-842-9_32","article-title":"IMGT(\u00ae) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT\/V-QUEST and IMGT\/HighV-QUEST for NGS","volume":"882","author":"Alamyar","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"2023070504575684400_B22","doi-asserted-by":"crossref","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":"2023070504575684400_B23","doi-asserted-by":"crossref","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":"2023070504575684400_B24","doi-asserted-by":"crossref","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":"2023070504575684400_B25","doi-asserted-by":"crossref","first-page":"e1004503","DOI":"10.1371\/journal.pcbi.1004503","article-title":"VDJtools: unifying post-analysis of T cell receptor repertoires","volume":"11","author":"Shugay","year":"2015","journal-title":"PLoS Comput. Biol."},{"key":"2023070504575684400_B26","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1534\/genetics.115.176735","article-title":"IMonitor: a robust pipeline for TCR and BCR repertoire analysis","volume":"201","author":"Zhang","year":"2015","journal-title":"Genetics"},{"key":"2023070504575684400_B27","doi-asserted-by":"crossref","first-page":"W264","DOI":"10.1093\/nar\/gky276","article-title":"BRepertoire: a user-friendly web server for analysing antibody repertoire data","volume":"46","author":"Margreitter","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023070504575684400_B28","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1080\/19420862.2015.1026502","article-title":"Reconstructing and mining the B cell repertoire with ImmunediveRsity","volume":"7","author":"Cortina-Ceballos","year":"2015","journal-title":"MAbs"},{"key":"2023070504575684400_B29","doi-asserted-by":"crossref","first-page":"e0166126","DOI":"10.1371\/journal.pone.0166126","article-title":"Vidjil: a web platform for analysis of high-throughput repertoire sequencing","volume":"11","author":"Duez","year":"2016","journal-title":"PLoS One"},{"key":"2023070504575684400_B30","doi-asserted-by":"crossref","first-page":"e1004409","DOI":"10.1371\/journal.pcbi.1004409","article-title":"Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation","volume":"12","author":"Ralph","year":"2016","journal-title":"PLoS Comput. Biol."},{"key":"2023070504575684400_B31","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":"2023070504575684400_B32","doi-asserted-by":"crossref","first-page":"176","DOI":"10.3389\/fimmu.2012.00176","article-title":"Immunoglobulin analysis tool: a novel tool for the analysis of human and mouse heavy and light chain transcripts","volume":"3","author":"Rogosch","year":"2012","journal-title":"Front. Immunol."},{"key":"2023070504575684400_B33","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1186\/s12859-015-0687-9","article-title":"ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT\/HighV-QUEST preprocessed NGS data","volume":"16","author":"Schaller","year":"2015","journal-title":"BMC Bioinf."},{"key":"2023070504575684400_B34","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/514550a","article-title":"The top 100 papers","volume":"514","author":"Van\u00a0Noorden","year":"2014","journal-title":"Nature"},{"key":"2023070504575684400_B35","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/978-1-4939-6622-6_8","article-title":"Multiple sequence alignment","volume":"1525","author":"Bawono","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"2023070504575684400_B36","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1007\/978-1-62703-646-7_6","article-title":"Clustal Omega, accurate alignment of very large numbers of sequences","volume":"1079","author":"Sievers","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"2023070504575684400_B37","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"2023070504575684400_B38","doi-asserted-by":"crossref","first-page":"6968","DOI":"10.1038\/s41467-022-34630-w","article-title":"Muscle5: high-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny","volume":"13","author":"Edgar","year":"2022","journal-title":"Nat. Commun."},{"key":"2023070504575684400_B39","doi-asserted-by":"crossref","first-page":"3939","DOI":"10.1093\/bioinformatics\/bty495","article-title":"PASTA for proteins","volume":"34","author":"Collins","year":"2018","journal-title":"Bioinformatics"},{"key":"2023070504575684400_B40","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1093\/sysbio\/syr095","article-title":"SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees","volume":"61","author":"Liu","year":"2012","journal-title":"Syst. Biol."},{"key":"2023070504575684400_B41","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1080\/10635150701472164","article-title":"Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments","volume":"56","author":"Talavera","year":"2007","journal-title":"Syst. Biol."},{"key":"2023070504575684400_B42","doi-asserted-by":"crossref","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":"2023070504575684400_B43","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1084\/jem.132.2.211","article-title":"An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity","volume":"132","author":"Wu","year":"1970","journal-title":"J. Exp. Med."},{"key":"2023070504575684400_B44","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1038\/342877a0","article-title":"Conformations of immunoglobulin hypervariable regions","volume":"342","author":"Chothia","year":"1989","journal-title":"Nature"},{"key":"2023070504575684400_B45","doi-asserted-by":"crossref","first-page":"D256","DOI":"10.1093\/nar\/gki010","article-title":"IMGT\/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes","volume":"33","author":"Giudicelli","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023070504575684400_B46","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1016\/j.sbi.2006.04.004","article-title":"Multiple sequence alignment","volume":"16","author":"Edgar","year":"2006","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023070504575684400_B47","doi-asserted-by":"crossref","first-page":"2295","DOI":"10.1093\/nar\/gkn072","article-title":"PROMALS3D: a tool for multiple protein sequence and structure alignments","volume":"36","author":"Pei","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023070504575684400_B48","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s13029-015-0039-1","article-title":"CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments","volume":"10","author":"Zhou","year":"2015","journal-title":"Source Code Biol. Med."},{"key":"2023070504575684400_B49","doi-asserted-by":"crossref","first-page":"D1140","DOI":"10.1093\/nar\/gkt1043","article-title":"SAbDab: the structural antibody database","volume":"42","author":"Dunbar","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023070504575684400_B50","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1016\/j.csbj.2020.03.011","article-title":"Caretta - A multiple protein structure alignment and feature extraction suite","volume":"18","author":"Akdel","year":"2020","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"2023070504575684400_B51","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.1093\/nar\/gki524","article-title":"TM-align: a protein structure alignment algorithm based on the TM-score","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023070504575684400_B52","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1002\/pro.4205","article-title":"Observed antibody space: a diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences","volume":"31","author":"Olsen","year":"2022","journal-title":"Protein Sci."},{"key":"2023070504575684400_B53","doi-asserted-by":"crossref","first-page":"3385","DOI":"10.1093\/bioinformatics\/btr587","article-title":"STRIKE: evaluation of protein msas using a single 3D structure","volume":"27","author":"Kemena","year":"2011","journal-title":"Bioinformatics"},{"key":"2023070504575684400_B54","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1093\/nar\/gkp1196","article-title":"Quality measures for protein alignment benchmarks","volume":"38","author":"Edgar","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023070504575684400_B55","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1002\/prot.20527","article-title":"BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark","volume":"61","author":"Thompson","year":"2005","journal-title":"Proteins"},{"key":"2023070504575684400_B56","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bib\/bbv099","article-title":"Multiple sequence alignment modeling: methods and applications","volume":"17","author":"Chatzou","year":"2016","journal-title":"Brief Bioinform"},{"key":"2023070504575684400_B57","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2013approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"2023070504575684400_B58","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1093\/molbev\/msw046","article-title":"ETE 3: reconstruction, analysis, and visualization of phylogenomic data","volume":"33","author":"Huerta-Cepas","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"2023070504575684400_B59","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res."},{"key":"2023070504575684400_B60","article-title":"Sequence logos for DNA sequence alignments","volume-title":"R Package Version","author":"Bembom","year":"2007"},{"key":"2023070504575684400_B61","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1109\/TVCG.2014.2346248","article-title":"UpSet: visualization of intersecting sets","volume":"20","author":"Lex","year":"2014","journal-title":"IEEE Trans... Vis. Comput. Graph."},{"key":"2023070504575684400_B62","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1038\/nmeth.2960","article-title":"Towards error-free profiling of immune repertoires","volume":"11","author":"Shugay","year":"2014","journal-title":"Nat. Methods"},{"key":"2023070504575684400_B63","doi-asserted-by":"crossref","first-page":"20140239","DOI":"10.1098\/rstb.2014.0239","article-title":"The analysis of clonal expansions in normal and autoimmune B cell repertoires","volume":"370","author":"Hershberg","year":"2015","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"2023070504575684400_B64","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1016\/j.it.2015.09.006","article-title":"Bioinformatic and statistical analysis of adaptive immune repertoires","volume":"36","author":"Greiff","year":"2015","journal-title":"Trends Immunol."},{"key":"2023070504575684400_B65","doi-asserted-by":"crossref","first-page":"899","DOI":"10.3389\/fimmu.2019.00899","article-title":"The pipeline repertoire for ig-seq analysis","volume":"10","author":"L\u00f3pez-Santib\u00e1\u00f1ez-J\u00e1come","year":"2019","journal-title":"Front. Immunol."},{"key":"2023070504575684400_B66","doi-asserted-by":"crossref","first-page":"170","DOI":"10.3389\/fimmu.2014.00170","article-title":"Reconstructing a B-cell clonal lineage. II. Mutation, selection, and affinity maturation","volume":"5","author":"Kepler","year":"2014","journal-title":"Front. Immunol."},{"key":"2023070504575684400_B67","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/s13073-015-0169-8","article-title":"A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status","volume":"7","author":"Greiff","year":"2015","journal-title":"Genome Med"},{"key":"2023070504575684400_B68","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1080\/01621459.1982.10477845","article-title":"Diversity as a concept and its measurement","volume":"77","author":"Patil","year":"1982","journal-title":"J. Am. Statist. Assoc."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W17\/50736510\/gkad400.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W17\/50736510\/gkad400.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T09:29:58Z","timestamp":1688549398000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/W1\/W17\/7173809"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,19]]},"references-count":68,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2023,5,19]]},"published-print":{"date-parts":[[2023,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkad400","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,5]]},"published":{"date-parts":[[2023,5,19]]}}}