{"id":"https://openalex.org/W3193928773","doi":"https://doi.org/10.1093/bioinformatics/btab788","title":"MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences","display_name":"MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences","publication_year":2021,"publication_date":"2021-11-12","ids":{"openalex":"https://openalex.org/W3193928773","doi":"https://doi.org/10.1093/bioinformatics/btab788","mag":"3193928773","pmid":"https://pubmed.ncbi.nlm.nih.gov/34791036"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab788","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab788","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/4/918/42319144/btab788.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","license_id":"https://openalex.org/licenses/cc-by","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/38/4/918/42319144/btab788.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032280221","display_name":"Chengze Shen","orcid":"https://orcid.org/0000-0003-2276-9892"},"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":false,"raw_author_name":"Chengze Shen","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA"],"raw_orcid":"https://orcid.org/0000-0003-2276-9892","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014969856","display_name":"Paul Zaharias","orcid":"https://orcid.org/0000-0003-3550-2636"},"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":false,"raw_author_name":"Paul Zaharias","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA"],"raw_orcid":"https://orcid.org/0000-0003-3550-2636","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032411541","display_name":"Tandy Warnow","orcid":"https://orcid.org/0000-0001-7717-3514"},"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":"Tandy Warnow","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA"],"raw_orcid":"https://orcid.org/0000-0001-7717-3514","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5032411541"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2584,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.79239809,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"38","issue":"4","first_page":"918","last_page":"924"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9645000100135803,"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":0.9645000100135803,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.00559999980032444,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.0044999998062849045,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/contig","display_name":"Contig","score":0.5838249325752258},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5751310586929321},{"id":"https://openalex.org/keywords/amplicon","display_name":"Amplicon","score":0.5532469749450684},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5488985180854797},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5136589407920837},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5028197169303894},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.48118311166763306},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.44337165355682373},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3904626965522766},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38002729415893555},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3766271770000458},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3346281051635742},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2794802188873291},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12405559420585632},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.08605030179023743},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0707148015499115}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.5838249325752258},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5751310586929321},{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.5532469749450684},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5488985180854797},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5136589407920837},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5028197169303894},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.48118311166763306},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.44337165355682373},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3904626965522766},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38002729415893555},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3766271770000458},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3346281051635742},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2794802188873291},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12405559420585632},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.08605030179023743},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0707148015499115},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab788","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab788","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/4/918/42319144/btab788.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34791036","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34791036","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:pubmedcentral.nih.gov:8796358","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8796358","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab788","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab788","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/4/918/42319144/btab788.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2952167421","display_name":null,"funder_award_id":"(OCI 07\u201025070)","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3000003317","display_name":"IIBR Informatics: Advancing Bioinformatics Methods using Ensembles of Profile Hidden Markov Models","funder_award_id":"2006069","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"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/G4911334988","display_name":"Sustained-Petascale In Action: Blue Waters Enabling Transformative Science And Engineering","funder_award_id":"1238993","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/W3193928773.pdf","grobid_xml":"https://content.openalex.org/works/W3193928773.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1748508858","https://openalex.org/W1775447850","https://openalex.org/W2007668764","https://openalex.org/W2031611770","https://openalex.org/W2033339460","https://openalex.org/W2097386339","https://openalex.org/W2107608009","https://openalex.org/W2113799994","https://openalex.org/W2125230147","https://openalex.org/W2127322768","https://openalex.org/W2132926880","https://openalex.org/W2140890018","https://openalex.org/W2141052558","https://openalex.org/W2142056356","https://openalex.org/W2147461064","https://openalex.org/W2147818576","https://openalex.org/W2156542082","https://openalex.org/W2159638180","https://openalex.org/W2160378127","https://openalex.org/W2337015246","https://openalex.org/W2549717400","https://openalex.org/W3044581192","https://openalex.org/W3109134151","https://openalex.org/W3122087892","https://openalex.org/W6658825153","https://openalex.org/W6674990016"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2378969149","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726"],"abstract_inverted_index":{"SUMMARY:":[0],"Multiple":[1],"sequence":[2,40],"alignment":[3,31,74,125,134,194],"is":[4,33,93,110,167,173],"an":[5,196],"initial":[6],"step":[7],"in":[8,24],"many":[9,100],"bioinformatics":[10],"pipelines,":[11],"including":[12,55],"phylogeny":[13],"estimation,":[14],"protein":[15],"structure":[16],"prediction":[17],"and":[18,43,102,117,171,189],"taxonomic":[19],"identification":[20],"of":[21,54,81,128,138,143,161],"reads":[22,56],"produced":[23],"amplicon":[25],"or":[26,57],"metagenomic":[27],"datasets,":[28],"etc.":[29],"Yet,":[30],"estimation":[32,75],"challenging":[34],"on":[35,149,169,175],"datasets":[36,47,77,157],"that":[37,68,86,103],"exhibit":[38],"substantial":[39,79],"length":[41],"heterogeneity,":[42],"especially":[44],"when":[45,76],"the":[46,118,124,141,151,186,192],"have":[48,69],"fragmentary":[49,82,97],"sequences":[50,98,120],"as":[51,195],"a":[52,88,105],"result":[53],"contigs":[58],"generated":[59],"by":[60,181],"next-generation":[61],"sequencing":[62],"technologies.":[63],"Here,":[64],"we":[65],"examine":[66],"techniques":[67],"been":[70],"developed":[71,90],"to":[72,96,112,184,198],"improve":[73],"contain":[78],"numbers":[80],"sequences.":[83],"We":[84],"find":[85],"MAGUS,":[87],"recently":[89],"MSA":[91],"method,":[92],"fairly":[94],"robust":[95],"under":[99],"conditions,":[101],"using":[104,126,191],"two-stage":[106],"approach":[107],"where":[108],"MAGUS":[109,139,172,183],"used":[111],"align":[113],"selected":[114],"'backbone":[115],"sequences'":[116],"remaining":[119],"are":[121,204],"added":[122],"into":[123],"ensembles":[127],"Hidden":[129],"Markov":[130],"Models":[131],"further":[132],"improves":[133,148],"accuracy.":[135],"The":[136],"combination":[137],"with":[140,158],"ensemble":[142],"eHMMs":[144],"(i.e.":[145],"MAGUS+eHMMs)":[146],"clearly":[147],"UPP,":[150],"previous":[152],"leading":[153],"method":[154],"for":[155],"aligning":[156],"high":[159],"levels":[160],"fragmentation.":[162],"AVAILABILITY":[163],"AND":[164],"IMPLEMENTATION:":[165],"UPP":[166],"available":[168,174,205],"https://github.com/smirarab/sepp,":[170],"https://github.com/vlasmirnov/MAGUS.":[176],"MAGUS+eHMMs":[177],"can":[178],"be":[179],"performed":[180],"running":[182],"obtain":[185],"backbone":[187,193],"alignment,":[188],"then":[190],"input":[197],"UPP.":[199],"SUPPLEMENTARY":[200],"INFORMATION:":[201],"Supplementary":[202],"data":[203],"at":[206],"Bioinformatics":[207],"online.":[208]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":9}],"updated_date":"2026-08-09T07:27:16.801131","created_date":"2025-10-10T00:00:00"}
