{"id":"https://openalex.org/W2170909437","doi":"https://doi.org/10.1093/bioinformatics/13.6.583","title":"Displaying the in formation contents of structural RNA alignments: the structure logos","display_name":"Displaying the in formation contents of structural RNA alignments: the structure logos","publication_year":1997,"publication_date":"1997-01-01","ids":{"openalex":"https://openalex.org/W2170909437","doi":"https://doi.org/10.1093/bioinformatics/13.6.583","mag":"2170909437","pmid":"https://pubmed.ncbi.nlm.nih.gov/9475985"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/13.6.583","doi":"https://doi.org/10.1093/bioinformatics/13.6.583","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/13.6.583","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/13/6/583/922283/13-6-583.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["abdc-a","cwts-core","poland-200"],"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"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/13/6/583/922283/13-6-583.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004614832","display_name":"Jan Gorodkin","orcid":"https://orcid.org/0000-0001-5823-4000","observed_orcids":["https://orcid.org/0000-0001-5823-4000"]},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"J. Gorodkin","raw_affiliation_strings":["Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark. gorodkin@cbs.dtu.dk","Center for Biological Sequence Analysis, The Technical University of Denmark, Building 206, 2800 Lyngby, DK-2800, Denmark and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark. gorodkin@cbs.dtu.dk","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"Center for Biological Sequence Analysis, The Technical University of Denmark, Building 206, 2800 Lyngby, DK-2800, Denmark and","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003136820","display_name":"Laurie J. Heyer","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]},{"id":"https://openalex.org/I2802236040","display_name":"University of Colorado System","ror":"https://ror.org/00jc20583","country_code":"US","type":"education","lineage":["https://openalex.org/I2802236040"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"L.J. Heyer","raw_affiliation_strings":["Department of Applied Mathematics University of Colorado Boulder, CO 80309, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics University of Colorado Boulder, CO 80309, USA","institution_ids":["https://openalex.org/I188538660","https://openalex.org/I2802236040"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011862057","display_name":"S\u00f8ren Brunak","orcid":"https://orcid.org/0000-0003-0316-5866","observed_orcids":["https://orcid.org/0000-0003-0316-5866"]},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"S. Brunak","raw_affiliation_strings":["Center for Biological Sequence Analysis, The Technical University of Denmark, Building 206, 2800 Lyngby, DK-2800, Denmark and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biological Sequence Analysis, The Technical University of Denmark, Building 206, 2800 Lyngby, DK-2800, Denmark and","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5097723873","display_name":"G.D. Storomo","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G.D. Storomo","raw_affiliation_strings":["Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, CO 80309, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, CO 80309, USA","institution_ids":["https://openalex.org/I188538660"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5004614832"],"corresponding_institution_ids":["https://openalex.org/I96673099"],"apc_list":null,"apc_paid":null,"fwci":0.7938,"has_fulltext":true,"cited_by_count":170,"citation_normalized_percentile":{"value":0.69624343,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"13","issue":"6","first_page":"583","last_page":"586"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9419000148773193,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9419000148773193,"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":0.04989999905228615,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.0017000000225380063,"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-logos","display_name":"sequence logos","score":0.9369999766349792},{"id":"https://openalex.org/keywords/rna-secondary-structure","display_name":"RNA secondary structure","score":0.7429999709129333},{"id":"https://openalex.org/keywords/rna-sequence-alignment","display_name":"RNA sequence alignment","score":0.6420000195503235},{"id":"https://openalex.org/keywords/mutual-information","display_name":"mutual information","score":0.7540000081062317},{"id":"https://openalex.org/keywords/base-pairing","display_name":"base pairing","score":0.9110000133514404}],"concepts":[{"id":"https://openalex.org/C150506046","wikidata":"https://www.wikidata.org/wiki/Q6667822","display_name":"Logos Bible Software","level":2,"score":0.815590500831604},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5427217483520508},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5241358876228333},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.49533334374427795},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4869872033596039},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4102102518081665},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35352039337158203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2747301459312439},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2156769037246704},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1071755588054657},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09220781922340393},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008433","descriptor_name":"Mathematics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009693","descriptor_name":"Nucleic Acid Hybridization","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/13.6.583","doi":"https://doi.org/10.1093/bioinformatics/13.6.583","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/13.6.583","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/13/6/583/922283/13-6-583.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["abdc-a","cwts-core","poland-200"],"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:9475985","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/9475985","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,"listed_in":[],"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":"Computer applications in the biosciences : CABIOS","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.324.5849","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.5849","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/13/6/583.full.pdf","raw_type":"text"},{"id":"pmh:oai:pure.atira.dk:publications/16a869a2-f62e-4acf-bde8-fcae7032dc17","doi":null,"is_oa":false,"landing_page_url":"https://orbit.dtu.dk/en/publications/16a869a2-f62e-4acf-bde8-fcae7032dc17","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Gorodkin , J , Heyer , L J , Brunak , S &amp; Stormo , G D 1997 , ' Displaying the information contents of structural RNA alignments: the structure logos ' , Computer Applications in the Biosciences , vol. 13 , no. 6 , pp. 583-586 .","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/13.6.583","doi":"https://doi.org/10.1093/bioinformatics/13.6.583","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/13.6.583","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/13/6/583/922283/13-6-583.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["abdc-a","cwts-core","poland-200"],"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"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3747809060","display_name":"DNA PATTERN IDENTIFICATION AND ANALYSIS","funder_award_id":"R01HG000249","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320320943","display_name":"Danmarks Grundforskningsfond","ror":"https://ror.org/00znyv691"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170909437.pdf","grobid_xml":"https://content.openalex.org/works/W2170909437.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W201917955","https://openalex.org/W1978202265","https://openalex.org/W2022108432","https://openalex.org/W2041877620","https://openalex.org/W2044442377","https://openalex.org/W2078640502","https://openalex.org/W2079321730","https://openalex.org/W2110455321","https://openalex.org/W2140651796","https://openalex.org/W2151538750","https://openalex.org/W2161381662","https://openalex.org/W6600011822"],"related_works":["https://openalex.org/W7096693925","https://openalex.org/W2138336530","https://openalex.org/W2159806560","https://openalex.org/W2041877620","https://openalex.org/W7096782845","https://openalex.org/W2132661997","https://openalex.org/W7100648326","https://openalex.org/W3144321627","https://openalex.org/W7100973472","https://openalex.org/W2070440246"],"abstract_inverted_index":{"MOTIVATION:":[0],"We":[1],"extend":[2],"the":[3,23,29,33,49,53,57,63,67,72,115],"standard":[4],"'Sequence":[5,88],"Logo'":[6],"method":[7],"of":[8,36,45,66],"Schneider":[9],"and":[10,31,70,94,106],"Stevens":[11],"(Nucleic":[12],"Acids":[13],"Res.,":[14],"18,":[15],"6097-6100,":[16],"1990)":[17],"to":[18,113],"incorporate":[19],"prior":[20,96],"frequencies":[21,97],"on":[22],"bases,":[24],"allow":[25],"for":[26],"gaps":[27,93],"in":[28,39,74,86],"alignments,":[30],"indicate":[32],"mutual":[34,64],"information":[35,58,65],"base-paired":[37],"regions":[38],"RNA.":[40],"RESULTS:":[41],"Given":[42],"an":[43,107],"alignment":[44],"RNA":[46],"sequences":[47],"with":[48],"base":[50,68,80],"pairings":[51],"indicated,":[52],"program":[54,116],"will":[55],"calculate":[56],"at":[59],"each":[60],"position,":[61],"including":[62],"pairs,":[69],"display":[71],"results":[73],"a":[75,87],"'Structure":[76],"Logo'.":[77],"Alignments":[78],"without":[79],"pairing":[81],"can":[82,110],"also":[83],"be":[84,111],"displayed":[85],"Logo',":[89],"but":[90],"still":[91],"allowing":[92],"incorporating":[95],"if":[98],"desired.":[99],"AVAILABILITY:":[100],"The":[101],"code":[102],"is":[103],"available":[104],"from,":[105],"Internet":[108],"server":[109],"used":[112],"run":[114],"at,":[117],"http://www.cbs.dtu.dk/gorodkin/appl/slogo.":[118],"html.":[119]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":10}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2016-06-24T00:00:00"}
