{"id":"https://openalex.org/W2139869862","doi":"https://doi.org/10.1093/bioinformatics/btm600","title":"BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence","display_name":"BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence","publication_year":2007,"publication_date":"2007-12-01","ids":{"openalex":"https://openalex.org/W2139869862","doi":"https://doi.org/10.1093/bioinformatics/btm600","mag":"2139869862","pmid":"https://pubmed.ncbi.nlm.nih.gov/18056064"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm600","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm600","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/424/50567920/bioinformatics_24_3_424.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/424/50567920/bioinformatics_24_3_424.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036642325","display_name":"Jacques Oberto","orcid":"https://orcid.org/0000-0003-1680-636X"},"institutions":[{"id":"https://openalex.org/I102197404","display_name":"Universit\u00e9 Paris-Sud","ror":"https://ror.org/028rypz17","country_code":"FR","type":"education","lineage":["https://openalex.org/I102197404"]},{"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/I4210135103","display_name":"Biology of Extremophiles Laboratory","ror":"https://ror.org/036mest28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I2738703131","https://openalex.org/I2738703131","https://openalex.org/I277688954","https://openalex.org/I4210106617","https://openalex.org/I4210113668","https://openalex.org/I4210114748","https://openalex.org/I4210135103","https://openalex.org/I4210139971"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Jacques Oberto","raw_affiliation_strings":["Biologie Mol\u00e9culaire du G\u00e8ne chez les Extr\u00eamophiles, Universit\u00e9 Paris-Sud, Institut de G\u00e9n\u00e9tique et Microbiologie, CNRS UMR8621, 91405 Orsay Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biologie Mol\u00e9culaire du G\u00e8ne chez les Extr\u00eamophiles, Universit\u00e9 Paris-Sud, Institut de G\u00e9n\u00e9tique et Microbiologie, CNRS UMR8621, 91405 Orsay Cedex, France","institution_ids":["https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I4210135103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5036642325"],"corresponding_institution_ids":["https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I4210135103"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.3813,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.61592009,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"24","issue":"3","first_page":"424","last_page":"425"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3603000044822693,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3603000044822693,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.10339999943971634,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.05209999904036522,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6968658566474915},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4938824772834778},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4843515157699585},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4602595269680023},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4601600170135498},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4477526843547821},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4393324553966522},{"id":"https://openalex.org/keywords/genbank","display_name":"GenBank","score":0.4312330484390259},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4195297360420227},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41644781827926636},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3394443392753601}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6968658566474915},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4938824772834778},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4843515157699585},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4602595269680023},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4601600170135498},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4477526843547821},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4393324553966522},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.4312330484390259},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4195297360420227},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41644781827926636},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3394443392753601},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btm600","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm600","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/424/50567920/bioinformatics_24_3_424.pdf","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:18056064","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18056064","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":"Journal Article"},{"id":"pmh:oai:HAL:hal-00264074v1","is_oa":false,"landing_page_url":"https://hal.science/hal-00264074","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":"Bioinformatics, 2008, 24 (3), pp.424-5. &#x27E8;10.1093/bioinformatics/btm600&#x27E9;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm600","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm600","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/424/50567920/bioinformatics_24_3_424.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2139869862.pdf"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W1984345785","https://openalex.org/W2161850605","https://openalex.org/W2169267759","https://openalex.org/W4248664566"],"related_works":["https://openalex.org/W2384605093","https://openalex.org/W2373528557","https://openalex.org/W2367416754","https://openalex.org/W2363678777","https://openalex.org/W2358341233","https://openalex.org/W2374910111","https://openalex.org/W2385611812","https://openalex.org/W2370466701","https://openalex.org/W2028473472","https://openalex.org/W2350041031"],"abstract_inverted_index":{"UNLABELLED:":[0],"BAGET":[1],"(Bacterial":[2],"and":[3,19,24,39,73,87],"Archaeal":[4],"Gene":[5],"Exploration":[6],"Tool)":[7],"is":[8,101],"a":[9,35,51,56,60,94,113],"web":[10],"service":[11],"designed":[12],"to":[13],"facilitate":[14],"extraction,":[15],"by":[16,93],"molecular":[17],"geneticists":[18],"phylogeneticists,":[20],"of":[21,34,43,59,64,71,78,82],"specific":[22],"gene":[23,45,70],"protein":[25],"sequences":[26],"from":[27],"completely":[28],"determined":[29],"prokaryotic":[30,37],"genomes.":[31],"Upon":[32],"selection":[33],"particular":[36],"organism":[38],"gene,":[40,81],"two":[41],"levels":[42],"visual":[44],"context":[46],"information":[47],"are":[48],"provided":[49,102],"on":[50,68],"single":[52],"dynamic":[53],"page:":[54],"(i)":[55],"graphical":[57],"representation":[58],"user":[61],"defined":[62],"portion":[63],"the":[65,69,75,79,83,88],"chromosome":[66],"centered":[67],"interest":[72],"(ii)":[74],"DNA":[76],"sequence":[77,100],"query":[80,105],"immediate":[84],"neighboring":[85],"genes":[86],"intergenic":[89],"regions":[90],"each":[91],"identified":[92],"consistent":[95],"color":[96],"code.":[97],"The":[98],"aminoacid":[99],"for":[103,121],"protein-coding":[104],"genes.":[106],"Query":[107],"results":[108],"can":[109],"be":[110],"exported":[111],"as":[112],"rich":[114],"text":[115],"format":[116],"(RTF)":[117],"word":[118],"processor":[119],"file":[120],"printing,":[122],"archival":[123],"or":[124],"further":[125],"analysis.":[126],"AVAILABILITY:":[127],"http://archaea.u-psud.fr/bin/baget.dll.":[128]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
