{"id":"https://openalex.org/W2159806560","doi":"https://doi.org/10.1093/nar/gkn258","title":"RNALogo: a new approach to display structural RNA alignment","display_name":"RNALogo: a new approach to display structural RNA alignment","publication_year":2008,"publication_date":"2008-05-21","ids":{"openalex":"https://openalex.org/W2159806560","doi":"https://doi.org/10.1093/nar/gkn258","mag":"2159806560","pmid":"https://pubmed.ncbi.nlm.nih.gov/18495753"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn258","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn258","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W91/18781347/gkn258.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W91/18781347/gkn258.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008637858","display_name":"Tzu\u2010Hao Chang","orcid":"https://orcid.org/0000-0001-7011-3754"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Tzu-Hao Chang","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan","National Central University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan","institution_ids":["https://openalex.org/I22265921"]},{"raw_affiliation_string":"National Central University","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016211165","display_name":"Jorng\u2010Tzong Horng","orcid":"https://orcid.org/0000-0002-7671-0573"},"institutions":[{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jorng-Tzong Horng","raw_affiliation_strings":["Department of Computer Science and Information Engineering,","Department of Life Science, National Central University, Chung-Li 320,","National Central University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering,","institution_ids":[]},{"raw_affiliation_string":"Department of Life Science, National Central University, Chung-Li 320,","institution_ids":["https://openalex.org/I22265921"]},{"raw_affiliation_string":"National Central University","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040277769","display_name":"Hsien\u2010Da Huang","orcid":"https://orcid.org/0000-0003-2857-7023"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]},{"id":"https://openalex.org/I22265921","display_name":"National Central University","ror":"https://ror.org/00944ve71","country_code":"TW","type":"education","lineage":["https://openalex.org/I22265921"]},{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN","TW"],"is_corresponding":false,"raw_author_name":"Hsien-Da Huang","raw_affiliation_strings":["Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan","Institute of Bioinformatics and","National Central University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan","institution_ids":["https://openalex.org/I148366613"]},{"raw_affiliation_string":"Institute of Bioinformatics and","institution_ids":["https://openalex.org/I4210148697"]},{"raw_affiliation_string":"National Central University","institution_ids":["https://openalex.org/I22265921"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.555,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.82441481,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"suppl_2","first_page":"W91","last_page":"W96"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/biology","display_name":"Biology","score":0.7530075311660767},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6928756237030029},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.564450204372406},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.4687393307685852},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.44379180669784546},{"id":"https://openalex.org/keywords/consensus-sequence","display_name":"Consensus sequence","score":0.4180021286010742},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4144919216632843},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.41377946734428406},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39021214842796326},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36045849323272705},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.27319157123565674},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2124355435371399},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.19100430607795715}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7530075311660767},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6928756237030029},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.564450204372406},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.4687393307685852},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.44379180669784546},{"id":"https://openalex.org/C54985914","wikidata":"https://www.wikidata.org/wiki/Q1295754","display_name":"Consensus sequence","level":4,"score":0.4180021286010742},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4144919216632843},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.41377946734428406},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39021214842796326},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36045849323272705},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.27319157123565674},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2124355435371399},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.19100430607795715}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkn258","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn258","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W91/18781347/gkn258.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:18495753","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18495753","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2447718","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2447718","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2447718/pdf/gkn258.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkn258","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn258","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W91/18781347/gkn258.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"},{"id":"https://openalex.org/F4320322724","display_name":"Ministry of Education, India","ror":"https://ror.org/048xjjh50"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2159806560.pdf","grobid_xml":"https://content.openalex.org/works/W2159806560.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1502578435","https://openalex.org/W1543796220","https://openalex.org/W1976067984","https://openalex.org/W1992590388","https://openalex.org/W2010231172","https://openalex.org/W2041877620","https://openalex.org/W2042881722","https://openalex.org/W2063105344","https://openalex.org/W2099111195","https://openalex.org/W2106882534","https://openalex.org/W2112785261","https://openalex.org/W2132661997","https://openalex.org/W2151538750","https://openalex.org/W2158266834","https://openalex.org/W2169636286","https://openalex.org/W2170909437","https://openalex.org/W2409075727","https://openalex.org/W6714453948","https://openalex.org/W7074172428"],"related_works":["https://openalex.org/W4286462077","https://openalex.org/W2076804805","https://openalex.org/W2038598202","https://openalex.org/W2470187006","https://openalex.org/W2538843585","https://openalex.org/W4320486808","https://openalex.org/W2981588377","https://openalex.org/W4237817584","https://openalex.org/W3207591281","https://openalex.org/W3185103915"],"abstract_inverted_index":{"Regulatory":[0],"RNAs":[1],"play":[2],"essential":[3,7],"roles":[4],"in":[5,33,96,120,140],"many":[6],"biological":[8],"processes,":[9],"ranging":[10],"from":[11],"gene":[12],"regulation":[13],"to":[14,24,143],"protein":[15],"synthesis.":[16],"This":[17],"work":[18],"presents":[19],"a":[20,26,34,40,104,129],"web-based":[21],"tool,":[22],"RNALogo,":[23],"create":[25],"new":[27],"graphical":[28,79],"representation":[29],"of":[30,74,86,88,131,147],"the":[31,78,97],"patterns":[32],"multiple":[35],"RNA":[36,52,58,68,99,118,149],"sequence":[37,53],"alignment":[38,54],"with":[39,90],"consensus":[41,57,98],"structure.":[42,60,101],"The":[43],"RNALogo":[44,61,82,102,112,138,151],"graph":[45,83,113],"can":[46,134],"indicate":[47],"significant":[48],"features":[49],"within":[50],"an":[51],"and":[55,65,71,106,122],"its":[56],"secondary":[59,69,100],"extends":[62],"Sequence":[63],"logos,":[64],"specifically":[66],"incorporates":[67],"structures":[70],"mutual":[72],"information":[73],"base-paired":[75],"regions":[76],"into":[77,128],"representation.":[80],"Each":[81],"is":[84,114,152],"composed":[85],"stacks":[87],"letters,":[89],"one":[91],"stack":[92],"for":[93,116],"each":[94,117],"position":[95],"provides":[103],"convenient":[105],"high":[107],"configurable":[108],"logo":[109],"generator.":[110],"An":[111],"generated":[115,124],"family":[119],"Rfam,":[121],"these":[123],"logos":[125],"are":[126],"accumulated":[127],"gallery":[130,142],"RNALogo.":[132],"Users":[133],"search":[135],"or":[136],"browse":[137],"graphs":[139],"this":[141],"receive":[144],"additional":[145],"perspectives":[146],"known":[148],"families.":[150],"now":[153],"available":[154],"at:":[155],"http://rnalogo.mbc.nctu.edu.tw/.":[156]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":15},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":7}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
