{"id":"https://openalex.org/W2149859854","doi":"https://doi.org/10.1093/bioinformatics/btn144","title":"MACHOS: Markov clusters of homologous subsequences","display_name":"MACHOS: Markov clusters of homologous subsequences","publication_year":2008,"publication_date":"2008-06-27","ids":{"openalex":"https://openalex.org/W2149859854","doi":"https://doi.org/10.1093/bioinformatics/btn144","mag":"2149859854","pmid":"https://pubmed.ncbi.nlm.nih.gov/18586748"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn144","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/13/i77/49052476/bioinformatics_24_13_i77.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/13/i77/49052476/bioinformatics_24_13_i77.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027570038","display_name":"Simon Wong","orcid":"https://orcid.org/0000-0002-5503-4510"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Simon Wong","raw_affiliation_strings":["ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023552489","display_name":"Mark A. Ragan","orcid":"https://orcid.org/0000-0003-1672-7020"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Mark A. Ragan","raw_affiliation_strings":["ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5027570038"],"corresponding_institution_ids":["https://openalex.org/I165143802"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9826,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.75682898,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"24","issue":"13","first_page":"i77","last_page":"i85"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.666700005531311,"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":0.666700005531311,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.07769999653100967,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.07090000063180923,"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/structural-classification-of-proteins-database","display_name":"Structural Classification of Proteins database","score":0.6614450812339783},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.5892270803451538},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5811840295791626},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5099104642868042},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47137486934661865},{"id":"https://openalex.org/keywords/subsequence","display_name":"Subsequence","score":0.4618571996688843},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4601590633392334},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.44778570532798767},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.4224916100502014},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.4141063690185547},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.4115179777145386},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40190786123275757},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39317795634269714},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.23637935519218445},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21194976568222046},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14886918663978577},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13625040650367737},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1358458697795868}],"concepts":[{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.6614450812339783},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.5892270803451538},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5811840295791626},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5099104642868042},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47137486934661865},{"id":"https://openalex.org/C137877099","wikidata":"https://www.wikidata.org/wiki/Q1332977","display_name":"Subsequence","level":3,"score":0.4618571996688843},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4601590633392334},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.44778570532798767},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.4224916100502014},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.4141063690185547},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.4115179777145386},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40190786123275757},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39317795634269714},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.23637935519218445},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21194976568222046},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14886918663978577},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13625040650367737},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1358458697795868},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C34388435","wikidata":"https://www.wikidata.org/wiki/Q2267362","display_name":"Bounded function","level":2,"score":0.0}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btn144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn144","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/13/i77/49052476/bioinformatics_24_13_i77.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18586748","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18586748","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:CiteSeerX.psu:10.1.1.568.9307","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.568.9307","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/24/13/i77.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.776.4125","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.776.4125","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/3e/17/btn144.PMC2718622.pdf","raw_type":"text"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:178470","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2718622","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2718622","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn144","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/13/i77/49052476/bioinformatics_24_13_i77.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2149859854.pdf","grobid_xml":"https://content.openalex.org/works/W2149859854.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1488711241","https://openalex.org/W1510029899","https://openalex.org/W1534406401","https://openalex.org/W1608203529","https://openalex.org/W1766517752","https://openalex.org/W1978444265","https://openalex.org/W1980038204","https://openalex.org/W1987888790","https://openalex.org/W1997268601","https://openalex.org/W2007745123","https://openalex.org/W2014719716","https://openalex.org/W2023790301","https://openalex.org/W2029282790","https://openalex.org/W2035278976","https://openalex.org/W2040191060","https://openalex.org/W2041862730","https://openalex.org/W2055043387","https://openalex.org/W2059453880","https://openalex.org/W2087064593","https://openalex.org/W2087885007","https://openalex.org/W2089499735","https://openalex.org/W2099468911","https://openalex.org/W2109681892","https://openalex.org/W2111374837","https://openalex.org/W2112792893","https://openalex.org/W2113403117","https://openalex.org/W2116377237","https://openalex.org/W2121272213","https://openalex.org/W2121564430","https://openalex.org/W2124166542","https://openalex.org/W2128899444","https://openalex.org/W2130479394","https://openalex.org/W2136280642","https://openalex.org/W2141885858","https://openalex.org/W2144616092","https://openalex.org/W2145100181","https://openalex.org/W2154816072","https://openalex.org/W2159266221","https://openalex.org/W2161062388","https://openalex.org/W4210400672","https://openalex.org/W4210580032","https://openalex.org/W4211083314","https://openalex.org/W4245145908","https://openalex.org/W4316253355","https://openalex.org/W6677959896"],"related_works":["https://openalex.org/W2075451741","https://openalex.org/W2070693796","https://openalex.org/W2139240863","https://openalex.org/W2183523499","https://openalex.org/W2164753093","https://openalex.org/W2170171070","https://openalex.org/W1965827393","https://openalex.org/W4235848672","https://openalex.org/W1514151181","https://openalex.org/W2108067237"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,23],"classification":[2,178],"of":[3,26,36,56,63,74,130,137,186,189,206,221,233,236],"proteins":[4,28,190,223,237],"into":[5,102,123,210,224],"homologous":[6,64,104,138,212],"groups":[7,171],"(families)":[8],"allows":[9,228],"their":[10],"structure":[11],"and":[12,17,99,164,197],"function":[13],"to":[14,33,78,88,152,160],"be":[15],"analysed":[16],"compared":[18],"in":[19,214,239],"an":[20,60],"evolutionary":[21,234],"context.":[22],"modular":[24],"nature":[25],"eukaryotic":[27,114,222,240],"presents":[29],"a":[30,43,84,149,187,215,230],"considerable":[31],"challenge":[32],"the":[34,72,107,142,193,219,253],"delineation":[35],"families,":[37,147],"as":[38,71,116,258],"different":[39],"local":[40],"regions":[41],"within":[42],"single":[44],"protein":[45,90,121,207],"may":[46],"share":[47],"common":[48],"ancestry":[49],"with":[50],"distinct,":[51],"even":[52],"mutually":[53],"exclusive,":[54],"sets":[55],"homologs,":[57],"thereby":[58],"creating":[59],"intricate":[61],"web":[62,81],"relationships":[65],"if":[66],"full-length":[67],"sequences":[68,122],"are":[69,246,256],"taken":[70],"unit":[73],"evolution.":[75],"We":[76,132,180],"attempt":[77],"disentangle":[79],"this":[80],"by":[82,173,184],"developing":[83],"fully":[85,174],"automated":[86,175],"pipeline":[87],"delineate":[89],"subsequences":[91,139],"that":[92,191,199,217],"represent":[93],"sensible":[94],"units":[95],"for":[96,229,252],"homology":[97],"inference,":[98],"clustering":[100,109],"them":[101],"putatively":[103],"families":[105,126,157,163,213],"using":[106,148],"Markov":[108,135],"algorithm.":[110],"RESULTS:":[111],"Using":[112],"six":[113,254],"proteomes":[115,255],"input,":[117],"we":[118],"clustered":[119],"162,349":[120],"19,697-77,415":[124],"subsequence":[125,156],"depending":[127],"on":[128],"granularity":[129],"clustering.":[131],"validated":[133],"these":[134],"clusters":[136],"(MACHOS)":[140],"against":[141],"manually":[143],"curated":[144],"Pfam":[145],"domain":[146,162,176],"quality":[150,167],"measure":[151],"assess":[153],"overlap.":[154],"Our":[155],"correspond":[158],"well":[159],"known":[161],"achieve":[165],"higher":[166],"scores":[168],"than":[169],"do":[170],"generated":[172],"family":[177],"methods.":[179],"illustrate":[181],"our":[182,200],"approach":[183,227],"analysis":[185],"group":[188],"contains":[192],"glutamyl/glutaminyl-tRNA":[194],"synthetase":[195],"domain,":[196],"conclude":[198],"method":[201],"can":[202],"produce":[203],"high-coverage":[204],"decomposition":[205],"sequence":[208],"space":[209],"precise":[211],"way":[216],"takes":[218],"modularity":[220],"account.":[225],"This":[226],"fine-scale":[231],"examination":[232],"histories":[235],"encoded":[238],"genomes.":[241],"SUPPLEMENTARY":[242],"INFORMATION:":[243],"Supplementary":[244],"data":[245],"available":[247,257],"at":[248],"Bioinformatics":[249],"online.":[250],"MACHOS":[251],"FASTA-formatted":[259],"files:":[260],"http://research1t.imb.uq.edu.au/ragan/machos.":[261]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}