{"id":"https://openalex.org/W2120584922","doi":"https://doi.org/10.1093/bioinformatics/btu634","title":"Log-odds sequence logos","display_name":"Log-odds sequence logos","publication_year":2014,"publication_date":"2014-10-06","ids":{"openalex":"https://openalex.org/W2120584922","doi":"https://doi.org/10.1093/bioinformatics/btu634","mag":"2120584922","pmid":"https://pubmed.ncbi.nlm.nih.gov/25294922"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu634","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu634","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/324/49012845/bioinformatics_31_3_324.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","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/31/3/324/49012845/bioinformatics_31_3_324.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I4210105714","display_name":"Center for Human Genetics","ror":"https://ror.org/01gcrbc43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210105714"]},{"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":["1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 2 Center for Human Genetics Research and 3 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 2 Center for Human Genetics Research and 3 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238","https://openalex.org/I200719446","https://openalex.org/I4210105714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017645655","display_name":"John A. Capra","orcid":"https://orcid.org/0000-0001-9743-1795"},"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/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I4210105714","display_name":"Center for Human Genetics","ror":"https://ror.org/01gcrbc43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210105714"]},{"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":"John A. Capra","raw_affiliation_strings":["1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 2 Center for Human Genetics Research and 3 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 2 Center for Human Genetics Research and 3 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238","https://openalex.org/I200719446","https://openalex.org/I4210105714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088040720","display_name":"Aleksandar Stojmirovi\u0107","orcid":"https://orcid.org/0000-0003-0957-6893"},"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/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I4210105714","display_name":"Center for Human Genetics","ror":"https://ror.org/01gcrbc43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210105714"]},{"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":true,"raw_author_name":"Aleksandar Stojmirovi\u0107","raw_affiliation_strings":["1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 2 Center for Human Genetics Research and 3 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 2 Center for Human Genetics Research and 3 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238","https://openalex.org/I200719446","https://openalex.org/I4210105714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009953849","display_name":"David Landsman","orcid":"https://orcid.org/0000-0002-9819-6675"},"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/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I4210105714","display_name":"Center for Human Genetics","ror":"https://ror.org/01gcrbc43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210105714"]},{"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":"David Landsman","raw_affiliation_strings":["1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 2 Center for Human Genetics Research and 3 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 2 Center for Human Genetics Research and 3 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238","https://openalex.org/I200719446","https://openalex.org/I4210105714"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015061000","display_name":"Stephen F. Altschul","orcid":"https://orcid.org/0000-0003-2120-9631"},"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/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I4210105714","display_name":"Center for Human Genetics","ror":"https://ror.org/01gcrbc43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210105714"]},{"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":true,"raw_author_name":"Stephen F. Altschul","raw_affiliation_strings":["1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 2 Center for Human Genetics Research and 3 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 2 Center for Human Genetics Research and 3 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238","https://openalex.org/I200719446","https://openalex.org/I4210105714"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5015061000","https://openalex.org/A5088040720"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I200719446","https://openalex.org/I4210105714","https://openalex.org/I4210109390"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5693,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.67844465,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"31","issue":"3","first_page":"324","last_page":"331"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.23389999568462372,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.23389999568462372,"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":0.12970000505447388,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.10480000078678131,"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/context","display_name":"Context (archaeology)","score":0.68000328540802},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6610919833183289},{"id":"https://openalex.org/keywords/odds","display_name":"Odds","score":0.5970130562782288},{"id":"https://openalex.org/keywords/column","display_name":"Column (typography)","score":0.5655007362365723},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5426850914955139},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.4757116436958313},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.47562840580940247},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4328908324241638},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42238831520080566},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4201425313949585},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4188719391822815},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.24453705549240112},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.17960599064826965},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16804316639900208},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1572849452495575},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1330215036869049}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.68000328540802},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6610919833183289},{"id":"https://openalex.org/C143095724","wikidata":"https://www.wikidata.org/wiki/Q515895","display_name":"Odds","level":3,"score":0.5970130562782288},{"id":"https://openalex.org/C2780551164","wikidata":"https://www.wikidata.org/wiki/Q2306599","display_name":"Column (typography)","level":3,"score":0.5655007362365723},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5426850914955139},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.4757116436958313},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.47562840580940247},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4328908324241638},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42238831520080566},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4201425313949585},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4188719391822815},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24453705549240112},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.17960599064826965},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16804316639900208},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1572849452495575},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1330215036869049},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C126042441","wikidata":"https://www.wikidata.org/wiki/Q1324888","display_name":"Frame (networking)","level":2,"score":0.0},{"id":"https://openalex.org/C151956035","wikidata":"https://www.wikidata.org/wiki/Q1132755","display_name":"Logistic regression","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu634","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu634","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/324/49012845/bioinformatics_31_3_324.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25294922","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25294922","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:4318935","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4318935","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu634","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu634","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/324/49012845/bioinformatics_31_3_324.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","score":0.5,"display_name":"Peace, Justice and strong institutions"},{"id":"https://metadata.un.org/sdg/10","score":0.47999998927116394,"display_name":"Reduced inequalities"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309151","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2120584922.pdf","grobid_xml":"https://content.openalex.org/works/W2120584922.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1574109141","https://openalex.org/W1786753252","https://openalex.org/W1967293793","https://openalex.org/W1970999032","https://openalex.org/W1973578915","https://openalex.org/W1980557641","https://openalex.org/W1988670311","https://openalex.org/W1993548347","https://openalex.org/W1998300401","https://openalex.org/W2006681603","https://openalex.org/W2011301632","https://openalex.org/W2013989044","https://openalex.org/W2015292449","https://openalex.org/W2021863432","https://openalex.org/W2027542060","https://openalex.org/W2033775040","https://openalex.org/W2041877620","https://openalex.org/W2055043387","https://openalex.org/W2066167693","https://openalex.org/W2067853554","https://openalex.org/W2069883264","https://openalex.org/W2074703985","https://openalex.org/W2084787613","https://openalex.org/W2087064593","https://openalex.org/W2091273971","https://openalex.org/W2094519647","https://openalex.org/W2099111195","https://openalex.org/W2107757325","https://openalex.org/W2108649941","https://openalex.org/W2122665495","https://openalex.org/W2133312664","https://openalex.org/W2141818629","https://openalex.org/W2143210482","https://openalex.org/W2144609215","https://openalex.org/W2158266834","https://openalex.org/W2158714788","https://openalex.org/W2167257571","https://openalex.org/W2169636286","https://openalex.org/W2600349519","https://openalex.org/W3123545922","https://openalex.org/W6634375705"],"related_works":["https://openalex.org/W1604849300","https://openalex.org/W2766061861","https://openalex.org/W1604293003","https://openalex.org/W1979850356","https://openalex.org/W3005040438","https://openalex.org/W1520846789","https://openalex.org/W3124750890","https://openalex.org/W3186119517","https://openalex.org/W2500600905","https://openalex.org/W1529420443"],"abstract_inverted_index":{"MOTIVATION:":[0],"DNA":[1],"and":[2,25,80,98],"protein":[3,109],"patterns":[4],"are":[5,26,52,62,126,158],"usefully":[6],"represented":[7],"by":[8],"sequence":[9],"logos.":[10],"However,":[11],"the":[12,37,106,114,144],"methods":[13],"for":[14,28],"logo":[15,41,132],"generation":[16,133],"in":[17,105,128],"common":[18],"use":[19],"lack":[20],"a":[21,40,44,59,99],"proper":[22],"statistical":[23],"basis,":[24],"non-optimal":[27],"recognizing":[29],"functionally":[30],"relevant":[31,118],"alignment":[32,47],"columns.":[33],"RESULTS:":[34],"We":[35,86],"redefine":[36],"information":[38],"at":[39,138,160],"position":[42],"as":[43,65],"per-observation":[45],"multiple":[46],"log-odds":[48],"score.":[49],"Such":[50],"scores":[51],"positive":[53],"or":[54,69],"negative,":[55],"depending":[56],"on":[57,90],"whether":[58],"column's":[60],"observations":[61],"better":[63],"explained":[64],"arising":[66],"from":[67,149],"relatedness":[68],"chance.":[70],"Within":[71],"this":[72,150],"framework,":[73],"we":[74],"propose":[75],"distinct":[76],"normalized":[77],"maximum":[78],"likelihood":[79],"Bayesian":[81],"measures":[82,89,112,125],"of":[83,101,108,116,143],"column":[84],"information.":[85],"illustrate":[87],"these":[88],"High":[91],"Mobility":[92],"Group":[93],"B":[94],"(HMGB)":[95],"box":[96],"proteins":[97],"dataset":[100],"enzyme":[102],"alignments.":[103],"Particularly":[104],"context":[107],"alignments,":[110],"our":[111],"improve":[113],"discrimination":[115],"biologically":[117],"positions.":[119],"AVAILABILITY":[120],"AND":[121],"IMPLEMENTATION:":[122],"Our":[123],"new":[124],"implemented":[127],"an":[129],"open-source":[130],"Web-based":[131],"program,":[134],"which":[135],"is":[136,146],"available":[137,148,159],"http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/index.html.":[139],"A":[140],"stand-alone":[141],"version":[142],"program":[145],"also":[147],"site.":[151],"CONTACT:":[152],"altschul@ncbi.nlm.nih.gov":[153],"SUPPLEMENTARY":[154],"INFORMATION:":[155],"Supplementary":[156],"data":[157],"Bioinformatics":[161],"online.":[162]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}