{"id":"https://openalex.org/W3204504530","doi":"https://doi.org/10.1371/journal.pcbi.1008950","title":"Recursive MAGUS: Scalable and accurate multiple sequence alignment","display_name":"Recursive MAGUS: Scalable and accurate multiple sequence alignment","publication_year":2021,"publication_date":"2021-10-06","ids":{"openalex":"https://openalex.org/W3204504530","doi":"https://doi.org/10.1371/journal.pcbi.1008950","mag":"3204504530","pmid":"https://pubmed.ncbi.nlm.nih.gov/34613974"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008950","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008950","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1008950","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053130831","display_name":"Vladimir Smirnov","orcid":"https://orcid.org/0000-0002-7826-1214"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Vladimir Smirnov","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7826-1214","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053130831"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.8142,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.7144504,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"17","issue":"10","first_page":"e1008950","last_page":"e1008950"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9940999746322632,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9868000149726868,"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/scalability","display_name":"Scalability","score":0.7062184810638428},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6743959188461304},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6600228548049927},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.5884125232696533},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.587298572063446},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5347572565078735},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5097445845603943},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.45851680636405945},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4015727639198303},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3921697437763214},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36986613273620605},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2087339460849762},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07886070013046265},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.061463892459869385},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.0521942675113678},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.04840764403343201}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7062184810638428},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6743959188461304},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6600228548049927},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.5884125232696533},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.587298572063446},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5347572565078735},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5097445845603943},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.45851680636405945},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4015727639198303},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3921697437763214},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36986613273620605},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2087339460849762},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07886070013046265},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.061463892459869385},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0521942675113678},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.04840764403343201},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"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":"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":"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":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1008950","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008950","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:34613974","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34613974","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:1a480c7a4dfb430ea27f619c372f5ae6","is_oa":true,"landing_page_url":"https://doaj.org/article/1a480c7a4dfb430ea27f619c372f5ae6","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":"PLoS Computational Biology, Vol 17, Iss 10, p e1008950 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8523058","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8523058","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008950","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008950","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3750374216","display_name":"ABI Innovation: New methods for multiple sequence alignment with improved accuracy and scalability","funder_award_id":"1458652","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6756578768","display_name":null,"funder_award_id":"ABI-1458652","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":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1519266993","https://openalex.org/W1748508858","https://openalex.org/W2007668764","https://openalex.org/W2031611770","https://openalex.org/W2056251063","https://openalex.org/W2102502076","https://openalex.org/W2119362018","https://openalex.org/W2127322768","https://openalex.org/W2140872496","https://openalex.org/W2142056356","https://openalex.org/W2144362290","https://openalex.org/W2147461064","https://openalex.org/W2159638180","https://openalex.org/W2169602699","https://openalex.org/W2982461819","https://openalex.org/W2991142785","https://openalex.org/W3109134151","https://openalex.org/W3162593345"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W2038009067","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726"],"abstract_inverted_index":{"Multiple":[0],"sequence":[1,11],"alignment":[2,22,65,84],"tools":[3],"struggle":[4],"to":[5,51,62,71],"keep":[6],"pace":[7],"with":[8,56],"rapidly":[9],"growing":[10],"data,":[12],"as":[13],"few":[14],"methods":[15,66],"can":[16],"handle":[17],"large":[18,34],"datasets":[19,55,68],"while":[20],"maintaining":[21],"accuracy.":[23],"We":[24,59],"recently":[25],"introduced":[26],"MAGUS,":[27],"a":[28,43],"new":[29],"state-of-the-art":[30],"method":[31],"for":[32],"aligning":[33],"numbers":[35],"of":[36,46,69,80],"sequences.":[37,74],"In":[38],"this":[39],"paper,":[40],"we":[41],"present":[42],"comprehensive":[44],"set":[45],"enhancements":[47],"that":[48],"allow":[49],"MAGUS":[50,61,81,91],"align":[52],"vastly":[53],"larger":[54],"greater":[57],"speed.":[58,90],"compare":[60],"other":[63,83],"leading":[64],"on":[67],"up":[70],"one":[72],"million":[73],"Our":[75],"results":[76],"demonstrate":[77],"the":[78],"advantages":[79],"over":[82],"software":[85],"in":[86,95],"both":[87],"accuracy":[88],"and":[89],"is":[92],"freely":[93],"available":[94],"open-source":[96],"form":[97],"at":[98],"https://github.com/vlasmirnov/MAGUS.":[99]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}