{"id":"https://openalex.org/W2957503884","doi":"https://doi.org/10.1186/s12859-019-2973-4","title":"RAFTS3G: an efficient and versatile clustering software to analyses in large protein datasets","display_name":"RAFTS3G: an efficient and versatile clustering software to analyses in large protein datasets","publication_year":2019,"publication_date":"2019-07-15","ids":{"openalex":"https://openalex.org/W2957503884","doi":"https://doi.org/10.1186/s12859-019-2973-4","mag":"2957503884","pmid":"https://pubmed.ncbi.nlm.nih.gov/31307371"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2973-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2973-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2973-4","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","license_id":"https://openalex.org/licenses/cc-by","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/track/pdf/10.1186/s12859-019-2973-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039808607","display_name":"Bruno Thiago de Lima Nichio","orcid":"https://orcid.org/0000-0002-0196-6486"},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Bruno Thiago de Lima Nichio","raw_affiliation_strings":["Department of Biochemistry, Biological Sciences Sector - Federal University of Paran\u00e1 (UFPR), Curitiba, PR, Brazil","Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Biological Sciences Sector - Federal University of Paran\u00e1 (UFPR), Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]},{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000104914","display_name":"Aryel Marlus Repula de Oliveira","orcid":null},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Aryel Marlus Repula de Oliveira","raw_affiliation_strings":["Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029547433","display_name":"Camilla Reginatto De Pierri","orcid":"https://orcid.org/0000-0002-6114-1734"},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Camilla Reginatto de Pierri","raw_affiliation_strings":["Department of Biochemistry, Biological Sciences Sector - Federal University of Paran\u00e1 (UFPR), Curitiba, PR, Brazil","Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Biological Sciences Sector - Federal University of Paran\u00e1 (UFPR), Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]},{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056023448","display_name":"Let\u00edcia Graziela Costa Santos","orcid":null},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Leticia Graziela Costa Santos","raw_affiliation_strings":["Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060649731","display_name":"Alexandre Quadros Lejambre","orcid":null},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alexandre Quadros Lejambre","raw_affiliation_strings":["Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019189321","display_name":"Ricardo A. Vialle","orcid":"https://orcid.org/0000-0003-3311-4197"},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Ricardo Assun\u00e7\u00e3o Vialle","raw_affiliation_strings":["Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067316087","display_name":"Nilson Da Rocha Coimbra","orcid":"https://orcid.org/0000-0001-9407-4761"},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Nilson Ant\u00f4nio da Rocha Coimbra","raw_affiliation_strings":["Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004289660","display_name":"Dieval Guizelini","orcid":"https://orcid.org/0000-0002-1080-8586"},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Dieval Guizelini","raw_affiliation_strings":["Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054748542","display_name":"Jeroniza Nunes Marchaukoski","orcid":"https://orcid.org/0000-0002-5176-7055"},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Jeroniza Nunes Marchaukoski","raw_affiliation_strings":["Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Fabio de Oliveira Pedrosa","orcid":null},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Fabio de Oliveira Pedrosa","raw_affiliation_strings":["Department of Biochemistry, Biological Sciences Sector - Federal University of Paran\u00e1 (UFPR), Curitiba, PR, Brazil","Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","Department of Biochemistry, Biological Sciences Sector \u2013 Federal University of Paran\u00e1 (UFPR), Curitiba, PR, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Biological Sciences Sector - Federal University of Paran\u00e1 (UFPR), Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]},{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]},{"raw_affiliation_string":"Department of Biochemistry, Biological Sciences Sector \u2013 Federal University of Paran\u00e1 (UFPR), Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087379620","display_name":"Roberto Tadeu Raittz","orcid":"https://orcid.org/0000-0002-5271-991X"},"institutions":[{"id":"https://openalex.org/I52418104","display_name":"Universidade Federal do Paran\u00e1","ror":"https://ror.org/05syd6y78","country_code":"BR","type":"education","lineage":["https://openalex.org/I52418104"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Roberto Tadeu Raittz","raw_affiliation_strings":["Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil. raittz@ufpr.br","Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-5271-991X","affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil. raittz@ufpr.br","institution_ids":["https://openalex.org/I52418104"]},{"raw_affiliation_string":"Laboratory of Bioinformatics, Professional and Technical Education Sector from the Federal University of Paran\u00e1, Curitiba, PR, Brazil","institution_ids":["https://openalex.org/I52418104"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5087379620"],"corresponding_institution_ids":["https://openalex.org/I52418104"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.2276,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.51127393,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"1","first_page":"392","last_page":"392"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9995999932289124,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9976000189781189,"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/cluster-analysis","display_name":"Cluster analysis","score":0.827865719795227},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7326745986938477},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.7250108122825623},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.48148930072784424},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.47487255930900574},{"id":"https://openalex.org/keywords/consensus-clustering","display_name":"Consensus clustering","score":0.45099449157714844},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3620898723602295},{"id":"https://openalex.org/keywords/correlation-clustering","display_name":"Correlation clustering","score":0.36090975999832153},{"id":"https://openalex.org/keywords/cure-data-clustering-algorithm","display_name":"CURE data clustering algorithm","score":0.3529040515422821}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.827865719795227},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7326745986938477},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.7250108122825623},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.48148930072784424},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.47487255930900574},{"id":"https://openalex.org/C186767784","wikidata":"https://www.wikidata.org/wiki/Q5162841","display_name":"Consensus clustering","level":5,"score":0.45099449157714844},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3620898723602295},{"id":"https://openalex.org/C94641424","wikidata":"https://www.wikidata.org/wiki/Q5172845","display_name":"Correlation clustering","level":3,"score":0.36090975999832153},{"id":"https://openalex.org/C33704608","wikidata":"https://www.wikidata.org/wiki/Q5014717","display_name":"CURE data clustering algorithm","level":4,"score":0.3529040515422821},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-2973-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2973-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2973-4","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31307371","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31307371","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:doaj.org/article:b2773d0fe0e344969419c808173a62fc","is_oa":true,"landing_page_url":"https://doaj.org/article/b2773d0fe0e344969419c808173a62fc","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":"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, Vol 20, Iss 1, Pp 1-7 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6631606","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6631606","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2973-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2973-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2973-4","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320324953","display_name":"Universidade Federal do Paran\u00e1","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2957503884.pdf","grobid_xml":"https://content.openalex.org/works/W2957503884.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W598156564","https://openalex.org/W1900937478","https://openalex.org/W1992221283","https://openalex.org/W2096525273","https://openalex.org/W2110340112","https://openalex.org/W2124351063","https://openalex.org/W2130219916","https://openalex.org/W2135152200","https://openalex.org/W2154139219","https://openalex.org/W2156125289","https://openalex.org/W2161072217","https://openalex.org/W2171963266","https://openalex.org/W2262188337","https://openalex.org/W2273522830","https://openalex.org/W2407247987","https://openalex.org/W2416828819","https://openalex.org/W2510820101","https://openalex.org/W2528816092","https://openalex.org/W2562773385","https://openalex.org/W2568061956","https://openalex.org/W2568815643","https://openalex.org/W2579441661","https://openalex.org/W2581263128","https://openalex.org/W2592038517","https://openalex.org/W2617529804","https://openalex.org/W2617643752","https://openalex.org/W2758004011","https://openalex.org/W2761430568","https://openalex.org/W2766147358","https://openalex.org/W2772747611","https://openalex.org/W2781869913","https://openalex.org/W2798235127","https://openalex.org/W2853074481","https://openalex.org/W2888581595","https://openalex.org/W2898833900","https://openalex.org/W2950954328","https://openalex.org/W2951525247","https://openalex.org/W2953008890","https://openalex.org/W2963607348","https://openalex.org/W3136918052","https://openalex.org/W4239634997","https://openalex.org/W6713777247"],"related_works":["https://openalex.org/W1574003721","https://openalex.org/W2311450085","https://openalex.org/W2804957450","https://openalex.org/W2163488696","https://openalex.org/W3197105638","https://openalex.org/W4232587025","https://openalex.org/W3168918549","https://openalex.org/W2060220440","https://openalex.org/W2309230723","https://openalex.org/W2804498673"],"abstract_inverted_index":{"Clustering":[0],"methods":[1,73,78,176,225],"are":[2,64],"essential":[3],"to":[4,10,66,97,114,121,143,173,189,198,201,222,256,266],"partitioning":[5],"biological":[6,37,127,204,231,240],"samples":[7],"being":[8],"useful":[9],"minimize":[11,267],"the":[12,41,57,68,83,105,130,155,169,178,186,227,234,237,244,251,268],"information":[13,39,128,241],"complexity":[14],"in":[15,19,75,100,129,138,150,154,159,216,226],"large":[16,101,207,230],"datasets.":[17],"Tools":[18],"this":[20],"context":[21],"usually":[22],"generates":[23],"data":[24,232,271],"with":[25,273],"greed":[26],"algorithms":[27],"that":[28],"solves":[29],"some":[30,61],"Data":[31,98],"Mining":[32,99],"difficulties":[33],"which":[34,76,147,209,259],"can":[35],"degrade":[36],"relevant":[38],"during":[40],"clustering":[42,58,72,122,228],"process.":[43,277],"The":[44,135],"lack":[45],"of":[46,48,60,71,86,124,132,157,163,203,214,229,239,246,270],"standardization":[47],"metrics":[49],"and":[50,82,152,243,264],"consistent":[51,247],"bases":[52],"also":[53],"raises":[54],"questions":[55],"about":[56],"efficiency":[59,215],"methods.":[62],"Benchmarks":[63],"needed":[65],"explore":[67],"full":[69],"potential":[70],"-":[74,81],"alignment-free":[77],"stand":[79],"out":[80],"good":[84],"choice":[85,171],"dataset":[87],"makes":[88],"it":[89],"essentials.":[90],"Here":[91],"we":[92],"present":[93],"a":[94,119,160,211],"new":[95],"approach":[96],"protein":[102],"sequences":[103,205,258],"datasets,":[104,208],"Rapid":[106],"Alignment":[107],"Free":[108],"Tool":[109],"for":[110],"Sequences":[111],"Similarity":[112],"Search":[113],"Groups":[115],"(RAFTS":[116],"3":[117,166,194,219,275],"G),":[118],"method":[120],"aiming":[123],"losing":[125],"less":[126],"processes":[131],"generation":[133,156],"groups.":[134,248],"strategy":[136],"developed":[137],"our":[139],"algorithm":[140],"is":[141,168,196,210],"optimized":[142],"be":[144],"more":[145,181],"astringent":[146],"reflects":[148],"increase":[149],"accuracy":[151],"sensitivity":[153],"clusters":[158],"wide":[161],"range":[162],"similarity.":[164],"RAFTS":[165,193,218,274],"G":[167,195,220,276],"better":[170],"compared":[172,221],"three":[174],"main":[175],"when":[177],"user":[179],"wants":[180],"reliable":[182],"result":[183],"even":[184],"ignoring":[185],"ideal":[187],"threshold":[188],"clustering.":[190,217],"In":[191],"general,":[192],"able":[197],"group":[199],"up":[200,265],"millions":[202],"into":[206],"remarkable":[212],"option":[213],"other":[223],"\u201cstandard-gold\u201d":[224],"maintains":[233],"balance":[235],"between":[236],"reduction":[238],"redundancy":[242],"creation":[245],"We":[249],"bring":[250],"binary":[252],"search":[253],"concept":[254],"applied":[255],"grouped":[257],"shows":[260],"maintaining":[261],"sensitivity/accuracy":[262],"relation":[263],"time":[269],"generated":[272]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
