{"id":"https://openalex.org/W2100883458","doi":"https://doi.org/10.1093/nar/gkl237","title":"BAGEL: a web-based bacteriocin genome mining tool","display_name":"BAGEL: a web-based bacteriocin genome mining tool","publication_year":2006,"publication_date":"2006-07-01","ids":{"openalex":"https://openalex.org/W2100883458","doi":"https://doi.org/10.1093/nar/gkl237","mag":"2100883458","pmid":"https://pubmed.ncbi.nlm.nih.gov/16845009"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkl237","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl237","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W273/7623364/gkl237.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W273/7623364/gkl237.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000658415","display_name":"Anne de Jong","orcid":"https://orcid.org/0000-0002-7024-2334"},"institutions":[{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"A. de Jong","raw_affiliation_strings":["Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands","Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, the Netherlands","institution_ids":["https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024324359","display_name":"Sacha A. F. T. van Hijum","orcid":"https://orcid.org/0000-0003-0741-2991"},"institutions":[{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"S. A. F. T. van Hijum","raw_affiliation_strings":["Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute  PO Box 14, 9750 AA Haren, The Netherlands","Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute  PO Box 14, 9750 AA Haren, The Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, the Netherlands","institution_ids":["https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028125197","display_name":"Jetta J. E. Bijlsma","orcid":null},"institutions":[{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"J. J. E. Bijlsma","raw_affiliation_strings":["Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute  PO Box 14, 9750 AA Haren, The Netherlands","Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute  PO Box 14, 9750 AA Haren, The Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, the Netherlands","institution_ids":["https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024844426","display_name":"Jan Kok","orcid":"https://orcid.org/0000-0001-8259-1008"},"institutions":[{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"J. Kok","raw_affiliation_strings":["Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute  PO Box 14, 9750 AA Haren, The Netherlands","Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute  PO Box 14, 9750 AA Haren, The Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, the Netherlands","institution_ids":["https://openalex.org/I169381384"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017781414","display_name":"Oscar P. Kuipers","orcid":"https://orcid.org/0000-0001-5596-7735"},"institutions":[{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"O. P. Kuipers","raw_affiliation_strings":["Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute  PO Box 14, 9750 AA Haren, The Netherlands","Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute  PO Box 14, 9750 AA Haren, The Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, the Netherlands","institution_ids":["https://openalex.org/I169381384"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5000658415"],"corresponding_institution_ids":["https://openalex.org/I169381384"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":10.2604,"has_fulltext":true,"cited_by_count":291,"citation_normalized_percentile":{"value":0.98360777,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"34","issue":"Web Server","first_page":"W273","last_page":"W279"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10141","display_name":"Probiotics and Fermented Foods","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10141","display_name":"Probiotics and Fermented Foods","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12489","display_name":"Microbial Metabolites in Food Biotechnology","score":0.9936000108718872,"subfield":{"id":"https://openalex.org/subfields/2916","display_name":"Nutrition and Dietetics"},"field":{"id":"https://openalex.org/fields/29","display_name":"Nursing"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9897000193595886,"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/biology","display_name":"Biology","score":0.9368209838867188},{"id":"https://openalex.org/keywords/bacteriocin","display_name":"Bacteriocin","score":0.6968441009521484},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6179108023643494},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5525076389312744},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3985728621482849},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3598071336746216},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33286356925964355},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.20141595602035522},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1924547255039215},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.09527519345283508}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9368209838867188},{"id":"https://openalex.org/C115574571","wikidata":"https://www.wikidata.org/wiki/Q183119","display_name":"Bacteriocin","level":3,"score":0.6968441009521484},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6179108023643494},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5525076389312744},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3985728621482849},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3598071336746216},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33286356925964355},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.20141595602035522},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1924547255039215},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.09527519345283508}],"mesh":[{"descriptor_ui":"D001430","descriptor_name":"Bacteriocins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001430","descriptor_name":"Bacteriocins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001430","descriptor_name":"Bacteriocins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001430","descriptor_name":"Bacteriocins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001430","descriptor_name":"Bacteriocins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001430","descriptor_name":"Bacteriocins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","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":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","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":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkl237","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl237","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W273/7623364/gkl237.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16845009","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16845009","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pure.rug.nl:openaire_cris_publications/b5636eeb-8fb4-4ebd-84f2-709c1b2ae80b","is_oa":true,"landing_page_url":"https://research.rug.nl/en/publications/b5636eeb-8fb4-4ebd-84f2-709c1b2ae80b","pdf_url":null,"source":{"id":"https://openalex.org/S4306400420","display_name":"University of Groningen research database (University of Groningen / Centre for Information Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I169381384","host_organization_name":"University of Groningen","host_organization_lineage":["https://openalex.org/I169381384"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"de Jong, A, van Hijum, S A F T, Bijlsma, J J E, Kok, J & Kuipers, O P 2006, 'BAGEL : a web-based bacteriocin genome mining tool', Nucleic Acids Research, vol. 34, pp. W273-W279. https://doi.org/10.1093/nar/gkl237","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pure.rug.nl:publications/b5636eeb-8fb4-4ebd-84f2-709c1b2ae80b","is_oa":true,"landing_page_url":"https://hdl.handle.net/11370/b5636eeb-8fb4-4ebd-84f2-709c1b2ae80b","pdf_url":"https://pure.rug.nl/ws/files/6704827/2006NuclAcidsResdeJong.pdf","source":{"id":"https://openalex.org/S4306400420","display_name":"University of Groningen research database (University of Groningen / Centre for Information Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I169381384","host_organization_name":"University of Groningen","host_organization_lineage":["https://openalex.org/I169381384"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"de Jong, A, van Hijum, S A F T, Bijlsma, J J E, Kok, J & Kuipers, O P 2006, 'BAGEL : a web-based bacteriocin genome mining tool', Nucleic Acids Research, vol. 34, pp. W273-W279. https://doi.org/10.1093/nar/gkl237","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:338442","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1538908","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1538908","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkl237","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkl237","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl237","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W273/7623364/gkl237.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.5299999713897705,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100883458.pdf","grobid_xml":"https://content.openalex.org/works/W2100883458.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1532202009","https://openalex.org/W1543344293","https://openalex.org/W1598875902","https://openalex.org/W1730500298","https://openalex.org/W1966120465","https://openalex.org/W1967386006","https://openalex.org/W1978164115","https://openalex.org/W2009221323","https://openalex.org/W2035829686","https://openalex.org/W2055043387","https://openalex.org/W2057046895","https://openalex.org/W2057138984","https://openalex.org/W2066021029","https://openalex.org/W2071578025","https://openalex.org/W2097126166","https://openalex.org/W2099648162","https://openalex.org/W2104340345","https://openalex.org/W2108360478","https://openalex.org/W2117207469","https://openalex.org/W2120835264","https://openalex.org/W2123783735","https://openalex.org/W2133253129","https://openalex.org/W2154077609","https://openalex.org/W2154382675","https://openalex.org/W2159401663","https://openalex.org/W2160051618","https://openalex.org/W2162586168","https://openalex.org/W2321650209","https://openalex.org/W2783981376","https://openalex.org/W3002361334","https://openalex.org/W4236236547","https://openalex.org/W4249037006","https://openalex.org/W4250473955","https://openalex.org/W4250721369"],"related_works":["https://openalex.org/W2155375462","https://openalex.org/W4281649587","https://openalex.org/W2076298506","https://openalex.org/W2159675136","https://openalex.org/W2030565022","https://openalex.org/W2082887468","https://openalex.org/W2162623537","https://openalex.org/W136835770","https://openalex.org/W2019088376","https://openalex.org/W2023330867"],"abstract_inverted_index":{"A":[0],"common":[1],"problem":[2],"in":[3,83,106,160,171,180],"the":[4,12,30,107,133,142,145,149],"annotation":[5,108],"of":[6,14,38,110,122,144],"open":[7],"reading":[8],"frames":[9],"(ORFs)":[10],"is":[11,28,151,185],"identification":[13],"genes":[15,55,101,154],"that":[16,78,102,155],"are":[17,56,97,103],"functionally":[18],"similar":[19],"but":[20],"have":[21,115],"limited":[22],"or":[23],"no":[24],"sequence":[25,86,143],"homology.":[26],"This":[27,60],"particularly":[29],"case":[31],"for":[32,137,153],"bacteriocins,":[33],"a":[34,75,84,120],"very":[35],"diverse":[36],"group":[37],"antimicrobial":[39],"peptides":[40],"produced":[41],"by":[42,47,99],"bacteria":[43],"and":[44,92],"usually":[45],"encoded":[46,98],"small,":[48],"poorly":[49],"conserved":[50],"ORFs.":[51],"ORFs":[52,82],"surrounding":[53,146],"bacteriocin":[54,69,81,90,177],"often":[57,104],"biosynthetic":[58],"genes.":[59,70],"information":[61],"can":[62],"be":[63],"used":[64],"to":[65,174],"locate":[66],"putative":[67,80,176],"structural":[68],"Here,":[71],"we":[72,114],"describe":[73],"BAGEL,":[74],"web":[76],"server":[77],"identifies":[79],"DNA":[85],"using":[87,119],"novel,":[88],"knowledge-based":[89],"databases":[91],"motif":[93],"databases.":[94],"Many":[95],"bacteriocins":[96],"small":[100],"omitted":[105],"process":[109],"bacterial":[111,182],"genomes.":[112,183],"Thus,":[113],"implemented":[116],"ORF":[117,124],"detection":[118],"number":[121],"published":[123],"prediction":[125],"tools.":[126],"In":[127],"addition,":[128],"BAGEL":[129,169,184],"takes":[130],"into":[131],"account":[132],"genomic":[134],"context,":[135],"i.e.":[136],"each":[138],"potential":[139],"bacteriocin-encoding":[140],"ORF,":[141],"region":[147],"on":[148],"genome":[150],"analyzed":[152],"might":[156],"encode":[157],"proteins":[158],"involved":[159],"biosynthesis,":[161],"transport,":[162],"regulation":[163],"and/or":[164],"immunity.":[165],"These":[166],"innovations":[167],"make":[168],"unique":[170],"its":[172],"ability":[173],"detect":[175],"gene":[178],"clusters":[179],"(new)":[181],"freely":[186],"accessible":[187],"at:":[188],"http://bioinformatics.biol.rug.nl/websoftware/bagel.":[189]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":32},{"year":2021,"cited_by_count":33},{"year":2020,"cited_by_count":24},{"year":2019,"cited_by_count":17},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":7}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
