{"id":"https://openalex.org/W4396895261","doi":"https://doi.org/10.1186/s12859-024-05805-7","title":"PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome","display_name":"PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome","publication_year":2024,"publication_date":"2024-05-14","ids":{"openalex":"https://openalex.org/W4396895261","doi":"https://doi.org/10.1186/s12859-024-05805-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/38745271"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05805-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05805-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05805-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05805-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040231895","display_name":"Lara V\u00e1zquez-Gonz\u00e1lez","orcid":"https://orcid.org/0000-0002-0122-5266"},"institutions":[{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]},{"id":"https://openalex.org/I4210148771","display_name":"Instituto de Investigaci\u00f3n Sanitaria de Santiago","ror":"https://ror.org/05n7xcf53","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210148771"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Lara V\u00e1zquez-Gonz\u00e1lez","raw_affiliation_strings":["Centro Singular de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, R\u00faa de Jenaro de la Fuente Dom\u00ednguez, E15782, Santiago de Compostela, Spain. laram.vazquez@usc.es","Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain. laram.vazquez@usc.es"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Singular de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, R\u00faa de Jenaro de la Fuente Dom\u00ednguez, E15782, Santiago de Compostela, Spain. laram.vazquez@usc.es","institution_ids":["https://openalex.org/I200284239"]},{"raw_affiliation_string":"Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain. laram.vazquez@usc.es","institution_ids":["https://openalex.org/I4210148771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029590833","display_name":"Alba Regueira\u2010Iglesias","orcid":"https://orcid.org/0000-0002-6549-7738"},"institutions":[{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]},{"id":"https://openalex.org/I4210148771","display_name":"Instituto de Investigaci\u00f3n Sanitaria de Santiago","ror":"https://ror.org/05n7xcf53","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210148771"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alba Regueira-Iglesias","raw_affiliation_strings":["Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain","Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical Surgical Specialities, School of Medicine and Dentistry, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain","institution_ids":["https://openalex.org/I4210148771"]},{"raw_affiliation_string":"Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical Surgical Specialities, School of Medicine and Dentistry, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain","institution_ids":["https://openalex.org/I200284239"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013130394","display_name":"Carlos Balsa\u2010Castro","orcid":"https://orcid.org/0000-0001-7937-6673"},"institutions":[{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]},{"id":"https://openalex.org/I4210111807","display_name":"Center for Research in Molecular Medicine and Chronic Diseases","ror":"https://ror.org/0280bnq76","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111807"]},{"id":"https://openalex.org/I4210148771","display_name":"Instituto de Investigaci\u00f3n Sanitaria de Santiago","ror":"https://ror.org/05n7xcf53","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210148771"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Carlos Balsa-Castro","raw_affiliation_strings":["Centro Singular de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, R\u00faa de Jenaro de la Fuente Dom\u00ednguez, E15782, Santiago de Compostela, Spain","Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain","Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical Surgical Specialities, School of Medicine and Dentistry, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Singular de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, R\u00faa de Jenaro de la Fuente Dom\u00ednguez, E15782, Santiago de Compostela, Spain","institution_ids":["https://openalex.org/I200284239","https://openalex.org/I4210111807"]},{"raw_affiliation_string":"Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain","institution_ids":["https://openalex.org/I4210148771"]},{"raw_affiliation_string":"Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical Surgical Specialities, School of Medicine and Dentistry, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain","institution_ids":["https://openalex.org/I200284239"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082525488","display_name":"Nicol\u00e1s Vila-Blanco","orcid":"https://orcid.org/0000-0001-5865-9973"},"institutions":[{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]},{"id":"https://openalex.org/I4210111807","display_name":"Center for Research in Molecular Medicine and Chronic Diseases","ror":"https://ror.org/0280bnq76","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111807"]},{"id":"https://openalex.org/I4210148771","display_name":"Instituto de Investigaci\u00f3n Sanitaria de Santiago","ror":"https://ror.org/05n7xcf53","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210148771"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Nicol\u00e1s Vila-Blanco","raw_affiliation_strings":["Centro Singular de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, R\u00faa de Jenaro de la Fuente Dom\u00ednguez, E15782, Santiago de Compostela, Spain","Departamento de Electr\u00f3nica e Computaci\u00f3n, Escola T\u00e9cnica Superior de Enxe\u00f1ar\u00eda, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain","Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Singular de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, R\u00faa de Jenaro de la Fuente Dom\u00ednguez, E15782, Santiago de Compostela, Spain","institution_ids":["https://openalex.org/I200284239","https://openalex.org/I4210111807"]},{"raw_affiliation_string":"Departamento de Electr\u00f3nica e Computaci\u00f3n, Escola T\u00e9cnica Superior de Enxe\u00f1ar\u00eda, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain","institution_ids":["https://openalex.org/I200284239"]},{"raw_affiliation_string":"Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain","institution_ids":["https://openalex.org/I4210148771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080433628","display_name":"Inmaculada Tom\u00e1s","orcid":"https://orcid.org/0000-0002-3317-0853"},"institutions":[{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]},{"id":"https://openalex.org/I4210111807","display_name":"Center for Research in Molecular Medicine and Chronic Diseases","ror":"https://ror.org/0280bnq76","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111807"]},{"id":"https://openalex.org/I4210148771","display_name":"Instituto de Investigaci\u00f3n Sanitaria de Santiago","ror":"https://ror.org/05n7xcf53","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210148771"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Inmaculada Tom\u00e1s","raw_affiliation_strings":["Centro Singular de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, R\u00faa de Jenaro de la Fuente Dom\u00ednguez, E15782, Santiago de Compostela, Spain. inmaculada.tomas@usc.es","Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain. inmaculada.tomas@usc.es","Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical Surgical Specialities, School of Medicine and Dentistry, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain. inmaculada.tomas@usc.es"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Singular de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, R\u00faa de Jenaro de la Fuente Dom\u00ednguez, E15782, Santiago de Compostela, Spain. inmaculada.tomas@usc.es","institution_ids":["https://openalex.org/I200284239"]},{"raw_affiliation_string":"Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain. inmaculada.tomas@usc.es","institution_ids":["https://openalex.org/I4210148771"]},{"raw_affiliation_string":"Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical Surgical Specialities, School of Medicine and Dentistry, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain. inmaculada.tomas@usc.es","institution_ids":["https://openalex.org/I200284239","https://openalex.org/I4210111807"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075062131","display_name":"Mar\u0131\u0301a J. Carreira","orcid":"https://orcid.org/0000-0003-0532-2351"},"institutions":[{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]},{"id":"https://openalex.org/I4210148771","display_name":"Instituto de Investigaci\u00f3n Sanitaria de Santiago","ror":"https://ror.org/05n7xcf53","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210148771"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Mar\u00eda J. Carreira","raw_affiliation_strings":["Centro Singular de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, R\u00faa de Jenaro de la Fuente Dom\u00ednguez, E15782, Santiago de Compostela, Spain. mariajose.carreira@usc.es","Departamento de Electr\u00f3nica e Computaci\u00f3n, Escola T\u00e9cnica Superior de Enxe\u00f1ar\u00eda, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain. mariajose.carreira@usc.es","Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain. mariajose.carreira@usc.es"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Singular de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, R\u00faa de Jenaro de la Fuente Dom\u00ednguez, E15782, Santiago de Compostela, Spain. mariajose.carreira@usc.es","institution_ids":["https://openalex.org/I200284239"]},{"raw_affiliation_string":"Departamento de Electr\u00f3nica e Computaci\u00f3n, Escola T\u00e9cnica Superior de Enxe\u00f1ar\u00eda, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain. mariajose.carreira@usc.es","institution_ids":["https://openalex.org/I200284239"]},{"raw_affiliation_string":"Instituto de Investigaci\u00f3n Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain. mariajose.carreira@usc.es","institution_ids":["https://openalex.org/I4210148771"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5040231895","https://openalex.org/A5075062131","https://openalex.org/A5080433628"],"corresponding_institution_ids":["https://openalex.org/I200284239","https://openalex.org/I4210111807","https://openalex.org/I4210148771"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.2649,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.77845304,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"25","issue":"1","first_page":"189","last_page":"189"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10257","display_name":"Oral microbiology and periodontitis research","score":0.6644999980926514,"subfield":{"id":"https://openalex.org/subfields/3506","display_name":"Periodontics"},"field":{"id":"https://openalex.org/fields/35","display_name":"Dentistry"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10257","display_name":"Oral microbiology and periodontitis research","score":0.6644999980926514,"subfield":{"id":"https://openalex.org/subfields/3506","display_name":"Periodontics"},"field":{"id":"https://openalex.org/fields/35","display_name":"Dentistry"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.14069999754428864,"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/T10066","display_name":"Gut microbiota and health","score":0.07460000365972519,"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/amplicon","display_name":"Amplicon","score":0.7683265209197998},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.7134751081466675},{"id":"https://openalex.org/keywords/primer","display_name":"Primer (cosmetics)","score":0.6844090223312378},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6261496543884277},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5474697351455688},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49152836203575134},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48273295164108276},{"id":"https://openalex.org/keywords/amplicon-sequencing","display_name":"Amplicon sequencing","score":0.43619656562805176},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4089522361755371},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3591156601905823},{"id":"https://openalex.org/keywords/16s-ribosomal-rna","display_name":"16S ribosomal RNA","score":0.3440311849117279},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32034939527511597},{"id":"https://openalex.org/keywords/polymerase-chain-reaction","display_name":"Polymerase chain reaction","score":0.24184805154800415},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19059833884239197},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12196701765060425}],"concepts":[{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.7683265209197998},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7134751081466675},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.6844090223312378},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6261496543884277},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5474697351455688},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49152836203575134},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48273295164108276},{"id":"https://openalex.org/C2993206177","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon sequencing","level":4,"score":0.43619656562805176},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4089522361755371},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3591156601905823},{"id":"https://openalex.org/C42062724","wikidata":"https://www.wikidata.org/wiki/Q1209205","display_name":"16S ribosomal RNA","level":3,"score":0.3440311849117279},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32034939527511597},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.24184805154800415},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19059833884239197},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12196701765060425},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009055","descriptor_name":"Mouth","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009055","descriptor_name":"Mouth","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009055","descriptor_name":"Mouth","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009055","descriptor_name":"Mouth","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009055","descriptor_name":"Mouth","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05805-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05805-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05805-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38745271","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38745271","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11092261","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11092261","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11092261/pdf/12859_2024_Article_5805.pdf","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:09ebf4be42224c80b86b45cd8192f01c","is_oa":false,"landing_page_url":"https://doaj.org/article/09ebf4be42224c80b86b45cd8192f01c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-11 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05805-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05805-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05805-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1044294895","display_name":null,"funder_award_id":"ED481A","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G113891353","display_name":null,"funder_award_id":"IN606B","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G2601125725","display_name":null,"funder_award_id":"ED431G-2019/04","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G3876637791","display_name":null,"funder_award_id":"ED431G","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G3960995764","display_name":null,"funder_award_id":"IN606B-2023/005","funder_id":"https://openalex.org/F4320325108","funder_display_name":"Conseller\u00eda de Cultura, Educaci\u00f3n e Ordenaci\u00f3n Universitaria, Xunta de Galicia"},{"id":"https://openalex.org/G4789051072","display_name":"Identificaci\u00f3n de nuevos biomarcadores moleculares con elevada precisi\u00f3n diagn\u00f3stica para detectar la periodontitis no tratada y su respuesta al tratamiento","funder_award_id":"PI21/00588","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G550632238","display_name":null,"funder_award_id":"GRC2021","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G8708978062","display_name":null,"funder_award_id":"ED481A-2021","funder_id":"https://openalex.org/F4320325108","funder_display_name":"Conseller\u00eda de Cultura, Educaci\u00f3n e Ordenaci\u00f3n Universitaria, Xunta de Galicia"},{"id":"https://openalex.org/G936197553","display_name":null,"funder_award_id":"ED431G 2019/04","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320325108","display_name":"Conseller\u00eda de Cultura, Educaci\u00f3n e Ordenaci\u00f3n Universitaria, Xunta de Galicia","ror":"https://ror.org/03gq5rs15"},{"id":"https://openalex.org/F4320326655","display_name":"Xunta de Galicia","ror":"https://ror.org/0181xnw06"},{"id":"https://openalex.org/F4320334923","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4396895261.pdf"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1697616527","https://openalex.org/W1996423252","https://openalex.org/W2043489409","https://openalex.org/W2051190765","https://openalex.org/W2053767920","https://openalex.org/W2066783207","https://openalex.org/W2101821016","https://openalex.org/W2108718991","https://openalex.org/W2114850508","https://openalex.org/W2115701239","https://openalex.org/W2121748291","https://openalex.org/W2133701090","https://openalex.org/W2166787752","https://openalex.org/W2195724570","https://openalex.org/W2471803752","https://openalex.org/W2510766756","https://openalex.org/W2603394147","https://openalex.org/W2900746810","https://openalex.org/W2936807503","https://openalex.org/W2979990328","https://openalex.org/W3028431867","https://openalex.org/W4220953677","https://openalex.org/W4360601292","https://openalex.org/W4386100465"],"related_works":["https://openalex.org/W2506843120","https://openalex.org/W2945285105","https://openalex.org/W4390154386","https://openalex.org/W2306179760","https://openalex.org/W4206175384","https://openalex.org/W2890961259","https://openalex.org/W4256272196","https://openalex.org/W2954242328","https://openalex.org/W2728043704","https://openalex.org/W4286615072"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,53,116,138,175],"selection":[2],"of":[3,21,43,81,148,158],"primer":[4,45,47,124,141,170],"pairs":[5,125,142,171],"in":[6,102,126],"sequencing-based":[7],"research":[8],"can":[9],"greatly":[10],"influence":[11],"the":[12,15,28,41,61,79,97,103,120,127,135,146,156,168,180],"results,":[13],"highlighting":[14],"need":[16],"for":[17,83,145,172],"a":[18,35,56,89,159],"tool":[19,162],"capable":[20],"analysing":[22],"their":[23,70],"performance":[24,42],"in-silico":[25],"prior":[26],"to":[27,39,95,166],"sequencing":[29,51],"process.":[30],"We":[31],"therefore":[32],"propose":[33],"PrimerEvalPy,":[34],"Python-based":[36],"package":[37,54],"designed":[38],"test":[40,96],"any":[44,50],"or":[46],"pair":[48],"against":[49,105],"database.":[52],"calculates":[55],"coverage":[57,82,160],"metric":[58],"and":[59,73,114,151],"returns":[60],"amplicon":[62],"sequences":[63],"found,":[64],"along":[65],"with":[66,134],"information":[67],"such":[68,163],"as":[69,164],"average":[71],"start":[72],"end":[74],"positions.":[75],"It":[76],"also":[77],"allows":[78],"analysis":[80,161],"different":[84],"taxonomic":[85],"levels.":[86],"RESULTS:":[87],"As":[88],"case":[90],"study,":[91],"PrimerEvalPy":[92,165],"was":[93],"used":[94,100,123],"most":[98,121],"commonly":[99,122],"primers":[101],"literature":[104],"two":[106],"oral":[107,128,149],"16S":[108],"rRNA":[109],"gene":[110],"databases":[111],"containing":[112],"bacteria":[113,150],"archaea.":[115,152],"results":[117],"showed":[118],"that":[119],"cavity":[129],"did":[130],"not":[131],"match":[132],"those":[133],"highest":[136],"coverage.":[137],"best":[139,169],"performing":[140],"were":[143],"found":[144],"detection":[147],"CONCLUSIONS:":[153],"This":[154],"demonstrates":[155],"importance":[157],"find":[167],"specific":[173],"niches.":[174],"software":[176],"is":[177],"available":[178],"under":[179],"MIT":[181],"licence":[182],"at":[183],"https://gitlab.citius.usc.es/lara.vazquez/PrimerEvalPy":[184],".":[185]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
