{"id":"https://openalex.org/W2153242254","doi":"https://doi.org/10.1093/bioinformatics/btg109","title":"Generating consensus sequences from partialorder multiple sequence alignment graphs","display_name":"Generating consensus sequences from partialorder multiple sequence alignment graphs","publication_year":2003,"publication_date":"2003-05-21","ids":{"openalex":"https://openalex.org/W2153242254","doi":"https://doi.org/10.1093/bioinformatics/btg109","mag":"2153242254","pmid":"https://pubmed.ncbi.nlm.nih.gov/12761063"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg109","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg109","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102893850","display_name":"Christopher J. Lee","orcid":"https://orcid.org/0000-0002-2952-9202"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christopher Lee","raw_affiliation_strings":["UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute Department of Chemistry, University of California, Los Angeles, Los Angeles, CA 90095-1570, USA. leec@mbi.ucla.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute Department of Chemistry, University of California, Los Angeles, Los Angeles, CA 90095-1570, USA. leec@mbi.ucla.edu","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5102893850"],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.7104,"has_fulltext":false,"cited_by_count":103,"citation_normalized_percentile":{"value":0.83894801,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"19","issue":"8","first_page":"999","last_page":"1008"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.40130001306533813,"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/T10604","display_name":"RNA Research and Splicing","score":0.40130001306533813,"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":0.3140000104904175,"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":0.21529999375343323,"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/sequence","display_name":"Sequence (biology)","score":0.7157436609268188},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6436581015586853},{"id":"https://openalex.org/keywords/consensus-sequence","display_name":"Consensus sequence","score":0.5738593935966492},{"id":"https://openalex.org/keywords/order","display_name":"Order (exchange)","score":0.507689356803894},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.48552727699279785},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.439137727022171},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3920476734638214},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3715391457080841},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12882599234580994},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12511828541755676},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.12237399816513062},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.09767201542854309}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7157436609268188},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6436581015586853},{"id":"https://openalex.org/C54985914","wikidata":"https://www.wikidata.org/wiki/Q1295754","display_name":"Consensus sequence","level":4,"score":0.5738593935966492},{"id":"https://openalex.org/C182306322","wikidata":"https://www.wikidata.org/wiki/Q1779371","display_name":"Order (exchange)","level":2,"score":0.507689356803894},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.48552727699279785},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.439137727022171},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3920476734638214},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3715391457080841},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12882599234580994},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12511828541755676},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.12237399816513062},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.09767201542854309},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btg109","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg109","pdf_url":null,"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:12761063","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12761063","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:10.1.1.579.863","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.579.863","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/19/8/999.full.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4451127660","display_name":null,"funder_award_id":"MH65166","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1593309771","https://openalex.org/W1635391495","https://openalex.org/W1839674003","https://openalex.org/W1969051510","https://openalex.org/W1986891966","https://openalex.org/W1987820419","https://openalex.org/W1989192948","https://openalex.org/W1991968395","https://openalex.org/W1994154030","https://openalex.org/W1994915965","https://openalex.org/W1995693931","https://openalex.org/W1996387066","https://openalex.org/W1998300401","https://openalex.org/W2010638919","https://openalex.org/W2019654533","https://openalex.org/W2033310094","https://openalex.org/W2038617558","https://openalex.org/W2052831012","https://openalex.org/W2055043387","https://openalex.org/W2061280979","https://openalex.org/W2074582967","https://openalex.org/W2094031081","https://openalex.org/W2099982459","https://openalex.org/W2102122585","https://openalex.org/W2117328480","https://openalex.org/W2119923823","https://openalex.org/W2121016876","https://openalex.org/W2126653676","https://openalex.org/W2127392194","https://openalex.org/W2128256249","https://openalex.org/W2136651963","https://openalex.org/W2142113273","https://openalex.org/W2143447881","https://openalex.org/W2144662851","https://openalex.org/W2144975794","https://openalex.org/W2158714788","https://openalex.org/W2160875291","https://openalex.org/W2164429509","https://openalex.org/W2166498534","https://openalex.org/W2419320253","https://openalex.org/W3146331408","https://openalex.org/W3147254695"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W997010268","https://openalex.org/W2018010122","https://openalex.org/W2153242254","https://openalex.org/W2078298125","https://openalex.org/W2184990081","https://openalex.org/W3027238885"],"abstract_inverted_index":{"MOTIVATION:":[0],"Consensus":[1],"sequence":[2,10,14,53,126],"generation":[3],"is":[4,99,156],"important":[5],"in":[6],"many":[7],"kinds":[8],"of":[9,51,84,91,94],"analysis":[11,50],"ranging":[12],"from":[13,76,138],"assembly":[15],"to":[16,116,128],"profile-based":[17],"iterative":[18],"search":[19],"methods.":[20],"However,":[21],"how":[22],"can":[23,113,146],"a":[24,36,66,100],"consensus":[25,74,86],"be":[26,114],"constructed":[27],"when":[28],"its":[29,121],"inherent":[30],"assumption-that":[31],"the":[32,89,95],"aligned":[33],"sequences":[34,75,87,137],"form":[35],"single":[37],"linear":[38],"consensus-is":[39],"not":[40],"true?":[41],"RESULTS:":[42],"Partial":[43],"Order":[44],"Alignment":[45],"(POA)":[46],"enables":[47],"construction":[48],"and":[49,82,102,107,112,141],"multiple":[52,73],"alignments":[54,127],"as":[55],"directed":[56],"acyclic":[57],"graphs":[58],"containing":[59],"complex":[60,78,109],"branching":[61],"structure.":[62],"Here":[63],"we":[64],"present":[65],"dynamic":[67],"programming":[68],"algorithm":[69],"(heaviest_bundle)":[70],"for":[71,105,123],"generating":[72],"such":[77],"alignments.":[79],"The":[80,152],"number":[81],"relationships":[83],"these":[85],"reveals":[88],"degree":[90],"structural":[92],"complexity":[93],"source":[96,154],"alignment.":[97,118],"This":[98],"powerful":[101],"general":[103],"approach":[104],"analyzing":[106,124],"visualizing":[108],"alignment":[110],"structures,":[111],"applied":[115],"any":[117],"We":[119],"illustrate":[120],"value":[122],"expressed":[125],"detect":[129],"alternative":[130],"splicing,":[131],"reconstruct":[132],"full":[133],"length":[134],"mRNA":[135],"isoform":[136],"EST":[139],"fragments,":[140],"separate":[142],"paralog":[143],"mixtures":[144],"that":[145],"cause":[147],"incorrect":[148],"SNP":[149],"predictions.":[150],"AVAILABILITY:":[151],"heaviest_bundle":[153],"code":[155],"available":[157],"at":[158],"http://www.bioinformatics.ucla.edu/poa":[159]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
