{"id":"https://openalex.org/W2170157200","doi":"https://doi.org/10.1371/journal.pcbi.0030065","title":"Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering","display_name":"Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering","publication_year":2007,"publication_date":"2007-04-10","ids":{"openalex":"https://openalex.org/W2170157200","doi":"https://doi.org/10.1371/journal.pcbi.0030065","mag":"2170157200","pmid":"https://pubmed.ncbi.nlm.nih.gov/17432929"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0030065","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030065","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030065&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030065&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103135268","display_name":"Sebastian Will","orcid":"https://orcid.org/0000-0002-2376-9205"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sebastian Will","raw_affiliation_strings":["Bioinformatics Group, Institute of Computer Science, University of Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Institute of Computer Science, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047490071","display_name":"Kristin Reiche","orcid":"https://orcid.org/0000-0002-4452-4872"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kristin Reiche","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011771355","display_name":"Ivo L. Hofacker","orcid":"https://orcid.org/0000-0001-7132-0800"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Ivo L Hofacker","raw_affiliation_strings":["Department of Theoretical Chemistry, University of Vienna, Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Vienna, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016104736","display_name":"Peter F. Stadler","orcid":"https://orcid.org/0000-0002-5016-5191"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Peter F Stadler","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017672883","display_name":"Rolf Backofen","orcid":"https://orcid.org/0000-0001-8231-3323"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Rolf Backofen","raw_affiliation_strings":["Bioinformatics Group, Institute of Computer Science, University of Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Institute of Computer Science, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5017672883"],"corresponding_institution_ids":["https://openalex.org/I161046081"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":13.3844,"has_fulltext":true,"cited_by_count":519,"citation_normalized_percentile":{"value":0.99375853,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"3","issue":"4","first_page":"e65","last_page":"e65"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9997000098228455,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/computational-biology","display_name":"Computational biology","score":0.696735680103302},{"id":"https://openalex.org/keywords/small-nucleolar-rna","display_name":"Small nucleolar RNA","score":0.6907879114151001},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.636646568775177},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6137318015098572},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5494009852409363},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.5269356966018677},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4557989239692688},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.4493532180786133},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.4414251446723938},{"id":"https://openalex.org/keywords/small-rna","display_name":"Small RNA","score":0.43581125140190125},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4050028324127197},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2775636315345764},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26009902358055115},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11262398958206177}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.696735680103302},{"id":"https://openalex.org/C179255354","wikidata":"https://www.wikidata.org/wiki/Q284416","display_name":"Small nucleolar RNA","level":5,"score":0.6907879114151001},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.636646568775177},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6137318015098572},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5494009852409363},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.5269356966018677},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4557989239692688},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.4493532180786133},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.4414251446723938},{"id":"https://openalex.org/C2779341050","wikidata":"https://www.wikidata.org/wiki/Q24287527","display_name":"Small RNA","level":4,"score":0.43581125140190125},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4050028324127197},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2775636315345764},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26009902358055115},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11262398958206177}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002938","descriptor_name":"Ciona intestinalis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002938","descriptor_name":"Ciona intestinalis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002938","descriptor_name":"Ciona intestinalis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002938","descriptor_name":"Ciona intestinalis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.0030065","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030065","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030065&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:17432929","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17432929","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:info:fedora/oai:univie.ac.at:o:244552","is_oa":true,"landing_page_url":"https://phaidra.univie.ac.at/o:244552","pdf_url":null,"source":{"id":"https://openalex.org/S4306401993","display_name":"Phaidra (Universit\u00e4t Wien)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I129774422","host_organization_name":"University of Vienna","host_organization_lineage":["https://openalex.org/I129774422"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN:1545-7885","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:7a911d5427e5469d864465f49570ade5","is_oa":true,"landing_page_url":"https://doaj.org/article/7a911d5427e5469d864465f49570ade5","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 3, Iss 4, p e65 (2007)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2622280","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC1851984","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/152410","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Inferring_Noncoding_RNA_Families_and_Classes_by_Means_of_Genome_Scale_Structure_Based_Clustering/152410","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:1851984","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1851984","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.0030065","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030065","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030065&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170157200.pdf","grobid_xml":"https://content.openalex.org/works/W2170157200.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1522740115","https://openalex.org/W1577113140","https://openalex.org/W1593152236","https://openalex.org/W1622263187","https://openalex.org/W1822105579","https://openalex.org/W1909512798","https://openalex.org/W1967864248","https://openalex.org/W1974736226","https://openalex.org/W1984675364","https://openalex.org/W1992361112","https://openalex.org/W1992941735","https://openalex.org/W1994749285","https://openalex.org/W2001583934","https://openalex.org/W2009736453","https://openalex.org/W2018216725","https://openalex.org/W2039925764","https://openalex.org/W2042881722","https://openalex.org/W2079320648","https://openalex.org/W2095145214","https://openalex.org/W2095373580","https://openalex.org/W2099468911","https://openalex.org/W2106144124","https://openalex.org/W2106554405","https://openalex.org/W2108266886","https://openalex.org/W2115215562","https://openalex.org/W2122035121","https://openalex.org/W2127981985","https://openalex.org/W2128356721","https://openalex.org/W2134861301","https://openalex.org/W2136725005","https://openalex.org/W2137042854","https://openalex.org/W2137257434","https://openalex.org/W2140302584","https://openalex.org/W2146187633","https://openalex.org/W2151922790","https://openalex.org/W2158826174","https://openalex.org/W2161115392","https://openalex.org/W2161381662","https://openalex.org/W2166745309","https://openalex.org/W2167557255","https://openalex.org/W2170592981"],"related_works":["https://openalex.org/W2790152170","https://openalex.org/W2156617674","https://openalex.org/W4242611624","https://openalex.org/W2547129954","https://openalex.org/W1970757825","https://openalex.org/W2890134923","https://openalex.org/W2095206021","https://openalex.org/W3144341322","https://openalex.org/W2158875805","https://openalex.org/W2018458485"],"abstract_inverted_index":{"The":[0,95,131,157],"RFAM":[1],"database":[2],"defines":[3],"families":[4,107],"of":[5,9,32,43,60,70,89,98,120,135,142,169,189,203,256],"ncRNAs":[6,257],"by":[7,37],"means":[8],"sequence":[10],"similarities":[11],"that":[12,34,117,146],"are":[13,35],"sufficient":[14],"to":[15,105,150,198,232,260],"establish":[16],"homology.":[17],"In":[18,230],"some":[19],"cases,":[20],"such":[21],"as":[22,236],"microRNAs":[23],"and":[24,40,52,64,84,248,251],"box":[25],"H/ACA":[26],"snoRNAs,":[27],"functional":[28],"commonalities":[29],"define":[30],"classes":[31,124,255],"RNAs":[33,63,101,221],"characterized":[36],"structural":[38],"similarities,":[39],"typically":[41],"consist":[42],"multiple":[44],"RNA":[45,66,123,244],"families.":[46],"Recent":[47],"advances":[48],"in":[49,208,222],"high-throughput":[50],"transcriptomics":[51],"comparative":[53],"genomics":[54],"have":[55,92,179,195],"produced":[56],"very":[57],"large":[58],"sets":[59],"putative":[61,122],"noncoding":[62],"regulatory":[65],"signals.":[67],"For":[68],"many":[69],"them,":[71],"evidence":[72],"for":[73,128,258],"stabilizing":[74],"selection":[75],"acting":[76],"on":[77,186],"their":[78,90],"secondary":[79],"structures":[80,91],"has":[81,264],"been":[82,93,265],"derived,":[83],"at":[85],"least":[86],"approximate":[87],"models":[88],"computed.":[94],"overwhelming":[96],"majority":[97],"these":[99],"hypothetical":[100],"cannot":[102],"be":[103],"assigned":[104],"established":[106],"or":[108,175],"classes.":[109],"We":[110,178],"present":[111],"here":[112],"a":[113,139,167,199,237],"structure-based":[114,238],"clustering":[115,184],"approach":[116,185],"is":[118,147,159],"capable":[119],"extracting":[121],"from":[125],"genome-wide":[126],"surveys":[127],"structured":[129,206],"RNAs.":[130],"LocARNA":[132],"(local":[133],"alignment":[134],"RNA)":[136],"tool":[137],"implements":[138],"novel":[140,254],"variant":[141],"the":[143,170,182,187,190,209,240],"Sankoff":[144],"algorithm":[145],"sufficiently":[148],"fast":[149],"deal":[151],"with":[152,173],"several":[153,243,253],"thousand":[154],"candidate":[155],"sequences.":[156,177],"method":[158,241],"also":[160],"robust":[161],"against":[162],"false":[163],"positive":[164],"predictions,":[165],"i.e.,":[166],"contamination":[168],"input":[171],"data":[172],"unstructured":[174],"nonconserved":[176],"successfully":[180],"tested":[181],"LocARNA-based":[183],"sequences":[188],"RFAM-seed":[191],"alignments.":[192],"Furthermore,":[193],"we":[194],"applied":[196],"it":[197],"previously":[200],"published":[201],"set":[202],"3,332":[204],"predicted":[205],"elements":[207],"Ciona":[210,223],"intestinalis":[211],"genome":[212],"(Missal":[213],"K,":[214],"Rose":[215],"D,":[216],"Stadler":[217],"PF":[218],"(2005)":[219],"Noncoding":[220],"intestinalis.":[224],"Bioinformatics":[225],"21":[226],"(Supplement":[227],"2):":[228],"i77-i78).":[229],"addition":[231],"recovering,":[233],"e.g.,":[234],"tRNAs":[235],"class,":[239],"identifies":[242],"families,":[245],"including":[246],"microRNA":[247],"snoRNA":[249],"candidates,":[250],"suggests":[252],"which":[259],"date":[261],"no":[262],"representative":[263],"experimentally":[266],"characterized.":[267]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":29},{"year":2022,"cited_by_count":23},{"year":2021,"cited_by_count":29},{"year":2020,"cited_by_count":23},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":32},{"year":2017,"cited_by_count":29},{"year":2016,"cited_by_count":24},{"year":2015,"cited_by_count":31},{"year":2014,"cited_by_count":37},{"year":2013,"cited_by_count":31},{"year":2012,"cited_by_count":33}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}