{"id":"https://openalex.org/W2066167693","doi":"https://doi.org/10.1371/journal.pcbi.1000852","title":"The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment","display_name":"The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment","publication_year":2010,"publication_date":"2010-07-15","ids":{"openalex":"https://openalex.org/W2066167693","doi":"https://doi.org/10.1371/journal.pcbi.1000852","mag":"2066167693","pmid":"https://pubmed.ncbi.nlm.nih.gov/20657661"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000852","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000852","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000852&type=printable","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://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000852&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015061000","display_name":"Stephen F. Altschul","orcid":"https://orcid.org/0000-0003-2120-9631"},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stephen F. Altschul","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America. altschul@ncbi.nlm.nih.gov","National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America. altschul@ncbi.nlm.nih.gov","institution_ids":["https://openalex.org/I4210109390"]},{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110276911","display_name":"John C. Wootton","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John C. Wootton","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029072664","display_name":"Elena Zaslavsky","orcid":"https://orcid.org/0000-0002-4828-7771"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elena Zaslavsky","raw_affiliation_strings":["Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080970152","display_name":"Yi\u2010Kuo Yu","orcid":"https://orcid.org/0000-0002-6213-7665"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi-Kuo Yu","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5015061000"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.5858,"has_fulltext":true,"cited_by_count":68,"citation_normalized_percentile":{"value":0.89588605,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"6","issue":"7","first_page":"e1000852","last_page":"e1000852"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9979000091552734,"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":0.9948999881744385,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/odds","display_name":"Odds","score":0.7063342332839966},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.6502434611320496},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.613736093044281},{"id":"https://openalex.org/keywords/substitution","display_name":"Substitution (logic)","score":0.5525981783866882},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5371224880218506},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5332344174385071},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.524603009223938},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5168443322181702},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5092827081680298},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.47606486082077026},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41840866208076477},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3760816752910614},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.363499253988266},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33280128240585327},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2754763960838318},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23376426100730896},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17845383286476135},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.09613373875617981},{"id":"https://openalex.org/keywords/logistic-regression","display_name":"Logistic regression","score":0.08631548285484314}],"concepts":[{"id":"https://openalex.org/C143095724","wikidata":"https://www.wikidata.org/wiki/Q515895","display_name":"Odds","level":3,"score":0.7063342332839966},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6502434611320496},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.613736093044281},{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.5525981783866882},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5371224880218506},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5332344174385071},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.524603009223938},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5168443322181702},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5092827081680298},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.47606486082077026},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41840866208076477},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3760816752910614},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.363499253988266},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33280128240585327},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2754763960838318},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23376426100730896},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17845383286476135},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.09613373875617981},{"id":"https://openalex.org/C151956035","wikidata":"https://www.wikidata.org/wiki/Q1132755","display_name":"Logistic regression","level":2,"score":0.08631548285484314},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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":"D000465","descriptor_name":"Algorithms","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":"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010961","descriptor_name":"Plasmodium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010961","descriptor_name":"Plasmodium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010961","descriptor_name":"Plasmodium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010961","descriptor_name":"Plasmodium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014122","descriptor_name":"Toxoplasma","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014122","descriptor_name":"Toxoplasma","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014122","descriptor_name":"Toxoplasma","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014122","descriptor_name":"Toxoplasma","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":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"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":"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},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1000852","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000852","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000852&type=printable","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:20657661","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20657661","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:RePEc:plo:pcbi00:1000852","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000852","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:e9faca37f8734d75922a832bf114517d","is_oa":true,"landing_page_url":"https://doaj.org/article/e9faca37f8734d75922a832bf114517d","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 6, Iss 7, p e1000852 (2010)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2000781","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2904766","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/142620","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/The_Construction_and_Use_of_Log_Odds_Substitution_Scores_for_Multiple_Sequence_Alignment/142620","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000852","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000852","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000852&type=printable","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":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G2150262284","display_name":null,"funder_award_id":"HHSN266200500021C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2066167693.pdf","grobid_xml":"https://content.openalex.org/works/W2066167693.grobid-xml"},"referenced_works_count":126,"referenced_works":["https://openalex.org/W11981056","https://openalex.org/W1500214331","https://openalex.org/W1501400124","https://openalex.org/W1519266993","https://openalex.org/W1548934951","https://openalex.org/W1566039206","https://openalex.org/W1574109141","https://openalex.org/W1590648220","https://openalex.org/W1607198972","https://openalex.org/W1694876563","https://openalex.org/W1966570126","https://openalex.org/W1967573783","https://openalex.org/W1969153299","https://openalex.org/W1970999032","https://openalex.org/W1973578915","https://openalex.org/W1975001431","https://openalex.org/W1979081881","https://openalex.org/W1983265703","https://openalex.org/W1985618229","https://openalex.org/W1998300401","https://openalex.org/W1998687409","https://openalex.org/W2003027767","https://openalex.org/W2004488542","https://openalex.org/W2004575181","https://openalex.org/W2005120335","https://openalex.org/W2006681603","https://openalex.org/W2008120462","https://openalex.org/W2009570821","https://openalex.org/W2011289056","https://openalex.org/W2013570924","https://openalex.org/W2014660704","https://openalex.org/W2015292449","https://openalex.org/W2016453697","https://openalex.org/W2017519756","https://openalex.org/W2019387703","https://openalex.org/W2019572077","https://openalex.org/W2021839440","https://openalex.org/W2027542060","https://openalex.org/W2028769673","https://openalex.org/W2031716828","https://openalex.org/W2033177501","https://openalex.org/W2033775040","https://openalex.org/W2035333716","https://openalex.org/W2036866029","https://openalex.org/W2037601368","https://openalex.org/W2038762649","https://openalex.org/W2041877620","https://openalex.org/W2043381551","https://openalex.org/W2048102092","https://openalex.org/W2051119339","https://openalex.org/W2053276922","https://openalex.org/W2056574818","https://openalex.org/W2062693912","https://openalex.org/W2065973977","https://openalex.org/W2066562848","https://openalex.org/W2068448872","https://openalex.org/W2074703985","https://openalex.org/W2076406620","https://openalex.org/W2076540369","https://openalex.org/W2083201277","https://openalex.org/W2085005062","https://openalex.org/W2085668020","https://openalex.org/W2086719212","https://openalex.org/W2087064593","https://openalex.org/W2090128221","https://openalex.org/W2092979861","https://openalex.org/W2094519647","https://openalex.org/W2095749144","https://openalex.org/W2097386339","https://openalex.org/W2099075703","https://openalex.org/W2099111195","https://openalex.org/W2099254366","https://openalex.org/W2101460669","https://openalex.org/W2102122585","https://openalex.org/W2106241755","https://openalex.org/W2106341787","https://openalex.org/W2106882534","https://openalex.org/W2107757325","https://openalex.org/W2107809511","https://openalex.org/W2109497857","https://openalex.org/W2110403456","https://openalex.org/W2112162865","https://openalex.org/W2115399262","https://openalex.org/W2118581189","https://openalex.org/W2118601726","https://openalex.org/W2122665495","https://openalex.org/W2124838725","https://openalex.org/W2124871329","https://openalex.org/W2126144301","https://openalex.org/W2129448726","https://openalex.org/W2132926880","https://openalex.org/W2133121166","https://openalex.org/W2135326109","https://openalex.org/W2140244239","https://openalex.org/W2140872496","https://openalex.org/W2141885858","https://openalex.org/W2143210482","https://openalex.org/W2143357251","https://openalex.org/W2144609215","https://openalex.org/W2145268834","https://openalex.org/W2147301280","https://openalex.org/W2147667050","https://openalex.org/W2148450265","https://openalex.org/W2151631782","https://openalex.org/W2151831732","https://openalex.org/W2151904894","https://openalex.org/W2156179961","https://openalex.org/W2158714788","https://openalex.org/W2159021758","https://openalex.org/W2161299051","https://openalex.org/W2162800127","https://openalex.org/W2163860567","https://openalex.org/W2164652663","https://openalex.org/W2167257571","https://openalex.org/W2167673155","https://openalex.org/W2168508791","https://openalex.org/W2170945060","https://openalex.org/W2172085483","https://openalex.org/W2601913882","https://openalex.org/W3123545922","https://openalex.org/W3140968660","https://openalex.org/W3214380909","https://openalex.org/W4210323379","https://openalex.org/W4236413252","https://openalex.org/W6959871885","https://openalex.org/W7048060829"],"related_works":["https://openalex.org/W2029514038","https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W1985408726","https://openalex.org/W1482324242","https://openalex.org/W2088487249","https://openalex.org/W2187357871","https://openalex.org/W2141411672","https://openalex.org/W4389053053","https://openalex.org/W2903170547"],"abstract_inverted_index":{"Most":[0],"pairwise":[1,32],"and":[2,100,111,127,131,146,151,164,220],"multiple":[3,48,144,175,187],"sequence":[4,84,141],"alignment":[5,169,176,188],"programs":[6,189],"seek":[7],"alignments":[8],"with":[9],"optimal":[10,125],"scores.":[11,170,196],"Central":[12],"to":[13,47,53,76,83,95,138,193],"defining":[14],"such":[15],"scores":[16,23,35,60,78,98,120],"is":[17],"selecting":[18],"a":[19,140,143,172],"set":[20],"of":[21,38,66,114,124,136,149,159,167,209],"substitution":[22,34,59,183],"for":[24,79],"aligned":[25],"amino":[26],"acids":[27],"or":[28],"nucleotides.":[29],"For":[30],"local":[31],"alignment,":[33,110,145],"are":[36],"implicitly":[37],"log-odds":[39,45],"form.":[40],"We":[41,92,197],"now":[42],"extend":[43],"the":[44,112,134,147,157,165,207,214],"formalism":[46],"alignments,":[49],"using":[50],"Bayesian":[51],"methods":[52],"construct":[54],"\"BILD\"":[55],"(\"Bayesian":[56],"Integral":[57],"Log-odds\")":[58],"from":[61],"prior":[62],"distributions":[63],"describing":[64],"columns":[65],"related":[67,160],"letters.":[68],"This":[69],"approach":[70],"has":[71,88],"been":[72],"used":[73],"previously":[74],"only":[75],"define":[77],"aligning":[80],"individual":[81],"sequences":[82,161],"profiles,":[85],"but":[86],"it":[87],"much":[89],"broader":[90],"applicability.":[91],"describe":[93],"how":[94,199],"calculate":[96],"BILD":[97,119,195,201],"efficiently,":[99],"illustrate":[101,198],"their":[102],"uses":[103],"in":[104,142,217],"Gibbs":[105],"sampling":[106],"optimization":[107],"procedures,":[108],"gapped":[109],"construction":[113],"hidden":[115],"Markov":[116],"model":[117,129],"profiles.":[118],"enable":[121],"automated":[122],"selection":[123,148],"motif":[126],"domain":[128,216],"widths,":[130],"can":[132,190,205],"inform":[133],"decision":[135],"whether":[137],"include":[139,156],"insertion":[150],"deletion":[152],"locations.":[153],"Other":[154],"applications":[155],"classification":[158],"into":[162],"subfamilies,":[163],"definition":[166],"profile-profile":[168],"Although":[171],"fully":[173],"realized":[174],"program":[177],"must":[178],"rely":[179],"upon":[180],"more":[181],"than":[182],"scores,":[184],"many":[185],"existing":[186],"be":[191],"modified":[192],"employ":[194],"simple":[200],"score":[202],"based":[203],"strategies":[204],"enhance":[206],"recognition":[208],"DNA":[210],"binding":[211],"domains,":[212],"including":[213],"Api-AP2":[215],"Toxoplasma":[218],"gondii":[219],"Plasmodium":[221],"falciparum.":[222]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}