{"id":"https://openalex.org/W2518118492","doi":"https://doi.org/10.1093/bioinformatics/btw571","title":"The OGCleaner: filtering false-positive homology clusters","display_name":"The OGCleaner: filtering false-positive homology clusters","publication_year":2016,"publication_date":"2016-09-10","ids":{"openalex":"https://openalex.org/W2518118492","doi":"https://doi.org/10.1093/bioinformatics/btw571","mag":"2518118492","pmid":"https://pubmed.ncbi.nlm.nih.gov/27614349"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw571","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw571","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/1/125/25140242/btw571.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/1/125/25140242/btw571.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063608648","display_name":"Mao Fujimoto","orcid":"https://orcid.org/0000-0002-2020-935X"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"M Stanley Fujimoto","raw_affiliation_strings":["Computer Science Department, Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035045568","display_name":"Anton Suvorov","orcid":"https://orcid.org/0000-0003-3898-9195"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anton Suvorov","raw_affiliation_strings":["Department of Biology, Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036455379","display_name":"Nicholas O. Jensen","orcid":"https://orcid.org/0000-0002-1177-3418"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas O Jensen","raw_affiliation_strings":["Department of Biology, Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058435710","display_name":"Mark Clement","orcid":"https://orcid.org/0000-0003-4902-3521"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark J Clement","raw_affiliation_strings":["Computer Science Department, Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064637082","display_name":"Quinn Snell","orcid":"https://orcid.org/0000-0002-0579-612X"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Quinn Snell","raw_affiliation_strings":["Computer Science Department, Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079176557","display_name":"Seth Bybee","orcid":"https://orcid.org/0000-0001-6224-6303"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Seth M Bybee","raw_affiliation_strings":["Department of Biology, Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5063608648"],"corresponding_institution_ids":["https://openalex.org/I100005738"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5229,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.72197314,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"33","issue":"1","first_page":"125","last_page":"127"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9829000234603882,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9829000234603882,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9747999906539917,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9581999778747559,"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/homology","display_name":"Homology (biology)","score":0.5708236694335938},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5096385478973389},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5008876323699951},{"id":"https://openalex.org/keywords/sequence-homology","display_name":"Sequence homology","score":0.41060441732406616},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3288842439651489},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.328133225440979},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3032725751399994},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.19403472542762756},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1117699146270752}],"concepts":[{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.5708236694335938},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5096385478973389},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5008876323699951},{"id":"https://openalex.org/C2779315201","wikidata":"https://www.wikidata.org/wiki/Q414601","display_name":"Sequence homology","level":4,"score":0.41060441732406616},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3288842439651489},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.328133225440979},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3032725751399994},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.19403472542762756},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1117699146270752}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw571","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw571","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/1/125/25140242/btw571.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27614349","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27614349","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:33/1/125","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/33/1/125","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw571","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw571","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/1/125/25140242/btw571.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4699999988079071,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G6755165505","display_name":null,"funder_award_id":"award","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G919499961","display_name":null,"funder_award_id":"1265714","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2518118492.pdf","grobid_xml":"https://content.openalex.org/works/W2518118492.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W2008856488","https://openalex.org/W2011301426","https://openalex.org/W2061939373","https://openalex.org/W2101234009","https://openalex.org/W2110335151","https://openalex.org/W2114616367","https://openalex.org/W2116398954","https://openalex.org/W2121743800","https://openalex.org/W2125359798","https://openalex.org/W2146709375","https://openalex.org/W2149956330","https://openalex.org/W2154085147","https://openalex.org/W2160378127","https://openalex.org/W2162528766","https://openalex.org/W2230749025","https://openalex.org/W2284014940","https://openalex.org/W2316262244","https://openalex.org/W2342249984","https://openalex.org/W2917702074","https://openalex.org/W4233334497","https://openalex.org/W4301806080","https://openalex.org/W6675354045","https://openalex.org/W6676338640","https://openalex.org/W6678804063"],"related_works":["https://openalex.org/W2373327015","https://openalex.org/W2365352214","https://openalex.org/W2034554207","https://openalex.org/W2386533626","https://openalex.org/W2084391532","https://openalex.org/W3151890006","https://openalex.org/W2370259341","https://openalex.org/W2163211634","https://openalex.org/W2025026055","https://openalex.org/W2387627227"],"abstract_inverted_index":{"https://github.com/byucsl/ogcleaner":[0],"CONTACT:":[1],"sfujimoto@gmail.comSupplementary":[2],"information:":[3],"Supplementary":[4],"data":[5],"are":[6],"available":[7],"at":[8],"Bioinformatics":[9],"online.":[10]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
