{"id":"https://openalex.org/W2158686006","doi":"https://doi.org/10.1093/bioinformatics/bth945","title":"IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V\u2013J and V\u2013D\u2013J JUNCTIONs","display_name":"IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V\u2013J and V\u2013D\u2013J JUNCTIONs","publication_year":2004,"publication_date":"2004-07-19","ids":{"openalex":"https://openalex.org/W2158686006","doi":"https://doi.org/10.1093/bioinformatics/bth945","mag":"2158686006","pmid":"https://pubmed.ncbi.nlm.nih.gov/15262823"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth945","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth945","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111391171","display_name":"Mehdi Yousfi Monod","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210114166","display_name":"Institut de G\u00e9n\u00e9tique Mol\u00e9culaire de Montpellier","ror":"https://ror.org/02785qs39","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210096427","https://openalex.org/I4210114166"]},{"id":"https://openalex.org/I4210152518","display_name":"Laboratoire d'Informatique Gaspard-Monge","ror":"https://ror.org/04t50yk91","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I142631665","https://openalex.org/I4210145102","https://openalex.org/I4210152518","https://openalex.org/I4210154111","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210163339","display_name":"Institut de G\u00e9n\u00e9tique Humaine","ror":"https://ror.org/05ee10k25","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210096427","https://openalex.org/I4210163339"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Mehdi Yousfi Monod","raw_affiliation_strings":["Laboratoire d'ImmunoG\u00e9n\u00e9tique Mol\u00e9culaire LIGM, Universit\u00e9 Montpellier II, UPR CNRS 1142, Institut de G\u00e9n\u00e9tique Humaine IGH, Montpellier Cedex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire d'ImmunoG\u00e9n\u00e9tique Mol\u00e9culaire LIGM, Universit\u00e9 Montpellier II, UPR CNRS 1142, Institut de G\u00e9n\u00e9tique Humaine IGH, Montpellier Cedex 5, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210152518","https://openalex.org/I1294671590","https://openalex.org/I4210163339","https://openalex.org/I4210114166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002360024","display_name":"V\u00e9ronique Giudicelli","orcid":"https://orcid.org/0000-0002-2258-468X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"V\u00e9ronique Giudicelli","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004367739","display_name":"Denys Chaume","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Denys Chaume","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5058352965","display_name":"Marie\u2010Paule Lefranc","orcid":"https://orcid.org/0000-0003-0116-9353"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Marie-Paule Lefranc","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5111391171"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210114166","https://openalex.org/I4210152518","https://openalex.org/I4210163339"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.042,"has_fulltext":false,"cited_by_count":333,"citation_normalized_percentile":{"value":0.94699116,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"20","issue":"suppl_1","first_page":"i379","last_page":"i385"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9610000252723694,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9610000252723694,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11171","display_name":"Diabetes and associated disorders","score":0.013000000268220901,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11020","display_name":"Immune Cell Function and Interaction","score":0.004999999888241291,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/palindrome","display_name":"Palindrome","score":0.7431704998016357},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6653457880020142},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6371386051177979},{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.6141689419746399},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5475035309791565},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5368103981018066},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5269549489021301},{"id":"https://openalex.org/keywords/locus","display_name":"Locus (genetics)","score":0.4195789694786072},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.24249771237373352}],"concepts":[{"id":"https://openalex.org/C44667518","wikidata":"https://www.wikidata.org/wiki/Q12321","display_name":"Palindrome","level":4,"score":0.7431704998016357},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6653457880020142},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6371386051177979},{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.6141689419746399},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5475035309791565},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5368103981018066},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5269549489021301},{"id":"https://openalex.org/C84597430","wikidata":"https://www.wikidata.org/wiki/Q106227","display_name":"Locus (genetics)","level":3,"score":0.4195789694786072},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.24249771237373352},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005803","descriptor_name":"Genes, Immunoglobulin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005803","descriptor_name":"Genes, Immunoglobulin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005803","descriptor_name":"Genes, Immunoglobulin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007133","descriptor_name":"Immunoglobulin Joining Region","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007133","descriptor_name":"Immunoglobulin Joining Region","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007133","descriptor_name":"Immunoglobulin Joining Region","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015329","descriptor_name":"Gene Rearrangement, T-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015329","descriptor_name":"Gene Rearrangement, T-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015329","descriptor_name":"Gene Rearrangement, T-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bth945","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth945","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15262823","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15262823","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:lirmm-00108578v1","is_oa":false,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-00108578","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1367-4803","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5799999833106995,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W623638409","https://openalex.org/W1536522695","https://openalex.org/W1747312855","https://openalex.org/W2004707654","https://openalex.org/W2007550282","https://openalex.org/W2012621186","https://openalex.org/W2049631297","https://openalex.org/W2068378281","https://openalex.org/W2082947088","https://openalex.org/W2084286364","https://openalex.org/W2105273832","https://openalex.org/W2107838665","https://openalex.org/W2125604001","https://openalex.org/W2134539970","https://openalex.org/W2141535486","https://openalex.org/W2170479957"],"related_works":["https://openalex.org/W2136569355","https://openalex.org/W4214506306","https://openalex.org/W2940487742","https://openalex.org/W4323366524","https://openalex.org/W1980577621","https://openalex.org/W2477304139","https://openalex.org/W1986616196","https://openalex.org/W2619402950","https://openalex.org/W1677680917","https://openalex.org/W2083717313"],"abstract_inverted_index":{"MOTIVATION:":[0],"To":[1],"create":[2],"the":[3,22,25,30,33,42,45,54,68,99,106,113,119,123,127,139,142,146,152,156,171,175,179,183,192,209,218,226],"enormous":[4],"diversity":[5,27,36],"of":[6,32,49,67,126,158,185,197,206],"10(12)":[7],"immunoglobulins":[8],"(IG)":[9],"and":[10,38,56,78,89,101,129,133,165,174,216],"T":[11],"cell":[12],"receptors":[13],"(TR)":[14],"per":[15],"individual,":[16],"very":[17],"complex":[18,131],"mechanisms":[19],"occur":[20,59],"at":[21,47,138,230],"DNA":[23],"level:":[24],"combinatorial":[26,147],"results":[28],"from":[29,145,178,208,217,225],"junction":[31,69],"variable":[34],"(V),":[35],"(D)":[37],"joining":[39],"(J)":[40],"genes;":[41],"N-diversity":[43],"represents":[44,81],"addition":[46],"random":[48],"nucleotides":[50],"not":[51],"encoded":[52],"in":[53,60,75,97,155,199],"genome;":[55],"somatic":[57,186],"hypermutations":[58,187],"IG":[61,77,100,128,159],"rearranged":[62,76],"sequences.":[63],"The":[64],"accurate":[65],"annotation":[66],"between":[70],"V,":[71],"D,":[72],"J":[73],"genes":[74,143,154],"TR":[79,102,130,162],"sequences":[80],"therefore":[82],"a":[83,200],"huge":[84],"challenge":[85],"by":[86],"its":[87],"uniqueness":[88],"complexity.":[90],"We":[91],"developed":[92],"IMGT/JunctionAnalysis":[93,117,194,222],"to":[94,105],"analyse":[95],"automatically":[96],"detail":[98],"junctions,":[103],"according":[104],"IMGT":[107,227],"Scientific":[108],"chart":[109],"rules,":[110],"based":[111],"on":[112],"IMGT-ONTOLOGY":[114],"concepts.":[115],"RESULTS:":[116],"is":[118,195,223],"first":[120],"tool":[121],"for":[122,188],"detailed":[124],"analysis":[125],"V-J":[132],"V-D-J":[134],"JUNCTION(s).":[135],"It":[136,149,169,181],"delimits,":[137],"nucleotide":[140],"level,":[141],"resulting":[144,177],"diversity.":[148],"identifies":[150],"accurately":[151],"D":[153],"junctions":[157,207],"heavy":[160],"(IGH),":[161],"beta":[163],"(TRB)":[164],"delta":[166],"(TRD)":[167],"chains.":[168],"delimits":[170],"palindromic":[172],"P-REGION(s)":[173],"N-REGION(s)":[176],"N-diversity.":[180],"evaluates":[182],"number":[184,205],"each":[189],"gene,":[190],"within":[191],"JUNCTION.":[193],"capable":[196],"analysing,":[198],"single":[201],"run,":[202],"an":[203],"unlimited":[204],"same":[210,219],"species":[211],"(currently":[212],"human":[213],"or":[214],"mouse)":[215],"locus.":[220],"AVAILABILITY:":[221],"available":[224],"Home":[228],"page":[229],"http://imgt.cines.fr":[231]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":23},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":27},{"year":2017,"cited_by_count":25},{"year":2016,"cited_by_count":26},{"year":2015,"cited_by_count":29},{"year":2014,"cited_by_count":25},{"year":2013,"cited_by_count":17},{"year":2012,"cited_by_count":11}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
