{"id":"https://openalex.org/W2149379826","doi":"https://doi.org/10.1093/nar/gkl231","title":"RNAMST: efficient and flexible approach for identifying RNA structural homologs","display_name":"RNAMST: efficient and flexible approach for identifying RNA structural homologs","publication_year":2006,"publication_date":"2006-07-01","ids":{"openalex":"https://openalex.org/W2149379826","doi":"https://doi.org/10.1093/nar/gkl231","mag":"2149379826","pmid":"https://pubmed.ncbi.nlm.nih.gov/16845040"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkl231","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl231","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W423/7623320/gkl231.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/34/suppl_2/W423/7623320/gkl231.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":true,"raw_author_name":"T.-H. Chang","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan","Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan,"],"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":"Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan,","institution_ids":["https://openalex.org/I22265921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076407116","display_name":"Haidong Huang","orcid":"https://orcid.org/0000-0003-3755-0623"},"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"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"H.-D. Huang","raw_affiliation_strings":["Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan,","Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan,","Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan,","institution_ids":["https://openalex.org/I148366613"]},{"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, National Chiao Tung University, Hsin-Chu 300, Taiwan,","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110253810","display_name":"Tien-Min Chuang","orcid":null},"institutions":[{"id":"https://openalex.org/I165106657","display_name":"Chien Hsin University of Science and Technology","ror":"https://ror.org/05fbv4544","country_code":"TW","type":"education","lineage":["https://openalex.org/I165106657"]},{"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":"T.-N. Chuang","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan,","Department of Electronic Engineering, Ching-Yun University, Chung-Li 320, Taiwan,"],"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":"Department of Electronic Engineering, Ching-Yun University, Chung-Li 320, Taiwan,","institution_ids":["https://openalex.org/I165106657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109241486","display_name":"Dray\u2010Ming Shien","orcid":null},"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"]},{"id":"https://openalex.org/I65446980","display_name":"National Chin-Yi University of Technology","ror":"https://ror.org/040bs6h16","country_code":"TW","type":"education","lineage":["https://openalex.org/I65446980"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"D.-M. Shien","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan,","Department of Electronic Engineering, Chin Min Institute of Technology, Miao-Li, Taiwan and"],"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":"Department of Electronic Engineering, Chin Min Institute of Technology, Miao-Li, Taiwan and","institution_ids":["https://openalex.org/I65446980"]}]},{"author_position":"last","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":"J.-T. Horng","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan,","Department of Life Science, National Central University, Chung-Li 320, Taiwan"],"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":"Department of Life Science, National Central University, Chung-Li 320, Taiwan","institution_ids":["https://openalex.org/I22265921"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5008637858"],"corresponding_institution_ids":["https://openalex.org/I22265921"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.6359,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.66648017,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"34","issue":"Web Server","first_page":"W423","last_page":"W428"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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":1.0,"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/T11482","display_name":"RNA modifications and cancer","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/T10604","display_name":"RNA Research and Splicing","score":0.9998000264167786,"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/biology","display_name":"Biology","score":0.9470701813697815},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.636012077331543},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6084863543510437},{"id":"https://openalex.org/keywords/homologous-chromosome","display_name":"Homologous chromosome","score":0.598298192024231},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5072631239891052},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23883873224258423}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9470701813697815},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.636012077331543},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6084863543510437},{"id":"https://openalex.org/C64894306","wikidata":"https://www.wikidata.org/wiki/Q849622","display_name":"Homologous chromosome","level":3,"score":0.598298192024231},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5072631239891052},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23883873224258423}],"mesh":[{"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkl231","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl231","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W423/7623320/gkl231.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16845040","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16845040","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:europepmc.org:338349","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1538813","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.581.7589","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.581.7589","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/34/suppl_2/W423.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1538813","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkl231","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":null,"license_id":null,"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/gkl231","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl231","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W423/7623320/gkl231.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/W2149379826.pdf","grobid_xml":"https://content.openalex.org/works/W2149379826.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W2002664542","https://openalex.org/W2003787247","https://openalex.org/W2012690027","https://openalex.org/W2033713984","https://openalex.org/W2039820890","https://openalex.org/W2042881722","https://openalex.org/W2055902910","https://openalex.org/W2065398612","https://openalex.org/W2092454702","https://openalex.org/W2099819774","https://openalex.org/W2105070391","https://openalex.org/W2112814753","https://openalex.org/W2114001343","https://openalex.org/W2116507553","https://openalex.org/W2122282339","https://openalex.org/W2130978693","https://openalex.org/W2131459517","https://openalex.org/W2141157874","https://openalex.org/W2144548050","https://openalex.org/W2170949754","https://openalex.org/W4243142319"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2075550301"],"abstract_inverted_index":{"RNA":[0,24,37,46,53,59,94,99],"molecules":[1],"fold":[2],"into":[3],"characteristic":[4],"secondary":[5],"structures":[6],"for":[7,44,51,87],"their":[8],"diverse":[9],"functional":[10,32],"activities":[11],"such":[12],"as":[13],"post-translational":[14],"regulation":[15],"of":[16,21,91],"gene":[17],"expression.":[18],"Searching":[19],"homologs":[20,55,90],"a":[22,30,35,67,92],"pre-defined":[23,93],"structural":[25,38,54,95],"motif,":[26,39],"which":[27,79],"may":[28],"be":[29],"known":[31],"element":[33],"or":[34],"putative":[36],"can":[40],"provide":[41],"useful":[42],"information":[43],"deciphering":[45],"regulatory":[47],"mechanisms.":[48],"Since":[49],"searching":[50],"the":[52,57,73,107,112,117,143],"among":[56,97],"numerous":[58,98],"sequences":[60],"is":[61,80,139],"extremely":[62],"time-consuming,":[63],"this":[64],"work":[65],"develops":[66],"data":[68],"preprocessing":[69],"strategy":[70],"to":[71,110,121],"enhance":[72],"search":[74],"efficiency":[75],"and":[76,83,131,135],"presents":[77],"RNAMST,":[78],"an":[81],"efficient":[82],"flexible":[84,136],"web":[85,108,119,144],"server":[86,109,120],"rapidly":[88],"identifying":[89],"motif":[96],"sequences.":[100],"Intuitive":[101],"user":[102],"interface":[103],"are":[104],"provided":[105],"on":[106,142],"facilitate":[111],"predictive":[113],"analysis.":[114],"By":[115],"comparing":[116],"proposed":[118],"other":[122],"tools":[123],"developed":[124],"previously,":[125],"RNAMST":[126,138],"performs":[127],"remarkably":[128],"more":[129,133],"efficiently":[130],"provides":[132],"effective":[134],"functions.":[137],"now":[140],"available":[141],"at":[145],"http://bioinfo.csie.ncu.edu.tw/~rnamst/.":[146]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
