{"id":"https://openalex.org/W2124995041","doi":"https://doi.org/10.1093/bioinformatics/btq634","title":"PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences","display_name":"PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences","publication_year":2010,"publication_date":"2010-11-18","ids":{"openalex":"https://openalex.org/W2124995041","doi":"https://doi.org/10.1093/bioinformatics/btq634","mag":"2124995041","pmid":"https://pubmed.ncbi.nlm.nih.gov/21088024"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq634","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq634","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/2/211/48867992/bioinformatics_27_2_211.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/2/211/48867992/bioinformatics_27_2_211.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044386095","display_name":"Stefan E. Seemann","orcid":"https://orcid.org/0000-0002-2359-4927"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"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"]},{"id":"https://openalex.org/I2802916955","display_name":"Max Perutz Labs","ror":"https://ror.org/05cz70a34","country_code":"AT","type":"facility","lineage":["https://openalex.org/I2802916955"]},{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT","DE","DK"],"is_corresponding":false,"raw_author_name":"Stefan E. Seemann","raw_affiliation_strings":["1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany","institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I124055696","https://openalex.org/I76134821","https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079662525","display_name":"Andreas S. Richter","orcid":"https://orcid.org/0000-0002-4166-0991"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"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"]},{"id":"https://openalex.org/I2802916955","display_name":"Max Perutz Labs","ror":"https://ror.org/05cz70a34","country_code":"AT","type":"facility","lineage":["https://openalex.org/I2802916955"]},{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT","DE","DK"],"is_corresponding":false,"raw_author_name":"Andreas S. Richter","raw_affiliation_strings":["1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany","institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I124055696","https://openalex.org/I76134821","https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049682751","display_name":"Tanja Gesell","orcid":"https://orcid.org/0000-0002-0733-7605"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"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"]},{"id":"https://openalex.org/I2802916955","display_name":"Max Perutz Labs","ror":"https://ror.org/05cz70a34","country_code":"AT","type":"facility","lineage":["https://openalex.org/I2802916955"]},{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT","DE","DK"],"is_corresponding":false,"raw_author_name":"Tanja Gesell","raw_affiliation_strings":["1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany","institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I124055696","https://openalex.org/I76134821","https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017672883","display_name":"Rolf Backofen","orcid":"https://orcid.org/0000-0001-8231-3323"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"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"]},{"id":"https://openalex.org/I2802916955","display_name":"Max Perutz Labs","ror":"https://ror.org/05cz70a34","country_code":"AT","type":"facility","lineage":["https://openalex.org/I2802916955"]},{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT","DE","DK"],"is_corresponding":true,"raw_author_name":"Rolf Backofen","raw_affiliation_strings":["1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany","institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I124055696","https://openalex.org/I76134821","https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004614832","display_name":"Jan Gorodkin","orcid":"https://orcid.org/0000-0001-5823-4000"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"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"]},{"id":"https://openalex.org/I2802916955","display_name":"Max Perutz Labs","ror":"https://ror.org/05cz70a34","country_code":"AT","type":"facility","lineage":["https://openalex.org/I2802916955"]},{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT","DE","DK"],"is_corresponding":true,"raw_author_name":"Jan Gorodkin","raw_affiliation_strings":["1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for non-coding RNA in Technology and Health, 2IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark, 3Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany 4Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Dr. Bohr-Gasse 9, Vienna, 1030, Austria and 5Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Albertstrasse 19, Freiburg, 79104, Germany","institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I124055696","https://openalex.org/I76134821","https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5004614832","https://openalex.org/A5017672883"],"corresponding_institution_ids":["https://openalex.org/I124055696","https://openalex.org/I161046081","https://openalex.org/I2802916955","https://openalex.org/I76134821"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.9534,"has_fulltext":true,"cited_by_count":57,"citation_normalized_percentile":{"value":0.91437774,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"27","issue":"2","first_page":"211","last_page":"219"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9513999819755554,"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":0.9513999819755554,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0142000000923872,"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":0.007300000172108412,"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/computational-biology","display_name":"Computational biology","score":0.6147820949554443},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5739580392837524},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.48248958587646484},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.4747876524925232},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.43779346346855164},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.43327295780181885},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4330156445503235},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3330361843109131},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3122326135635376},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.17624306678771973},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11116737127304077},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.10975468158721924}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6147820949554443},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5739580392837524},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.48248958587646484},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.4747876524925232},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.43779346346855164},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.43327295780181885},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4330156445503235},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3330361843109131},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3122326135635376},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.17624306678771973},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11116737127304077},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.10975468158721924}],"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":"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","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":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btq634","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq634","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/2/211/48867992/bioinformatics_27_2_211.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21088024","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21088024","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3018821","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3018821","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/1b054535-ad62-45ba-98d2-0bb79f35cb89","is_oa":false,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/1b054535-ad62-45ba-98d2-0bb79f35cb89","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Seemann , E S , Richter , A S , Gesell , T , Backofen , R & Gorodkin , J 2011 , ' PETcofold : predicting conserved interactions and structures of two multiple alignments of RNA sequences ' , Bioinformatics , vol. 27 , no. 2 , pp. 211-219 . https://doi.org/10.1093/bioinformatics/btq634","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq634","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq634","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/2/211/48867992/bioinformatics_27_2_211.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1200370376","display_name":null,"funder_award_id":"EXC 294","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G3028935652","display_name":null,"funder_award_id":"EXC 294","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G894356745","display_name":null,"funder_award_id":"0313921","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321003","display_name":"Vienna Science and Technology Fund","ror":"https://ror.org/01f9mc681"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320321999","display_name":"Lundbeckfonden","ror":"https://ror.org/03hz8wd80"},{"id":"https://openalex.org/F4320327918","display_name":"H. Lundbeck A/S","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2124995041.pdf","grobid_xml":"https://content.openalex.org/works/W2124995041.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W30210889","https://openalex.org/W1501627602","https://openalex.org/W1543796220","https://openalex.org/W1873547760","https://openalex.org/W1974736226","https://openalex.org/W1975148447","https://openalex.org/W1976021976","https://openalex.org/W1978967539","https://openalex.org/W1983815263","https://openalex.org/W1992361112","https://openalex.org/W2004676196","https://openalex.org/W2008856488","https://openalex.org/W2009659958","https://openalex.org/W2016481001","https://openalex.org/W2024799598","https://openalex.org/W2025763720","https://openalex.org/W2039925764","https://openalex.org/W2043653977","https://openalex.org/W2045895660","https://openalex.org/W2053783019","https://openalex.org/W2054260432","https://openalex.org/W2062896692","https://openalex.org/W2064904514","https://openalex.org/W2074237174","https://openalex.org/W2085534636","https://openalex.org/W2088784401","https://openalex.org/W2092867893","https://openalex.org/W2094253263","https://openalex.org/W2098508116","https://openalex.org/W2099306789","https://openalex.org/W2102304447","https://openalex.org/W2102424972","https://openalex.org/W2104504949","https://openalex.org/W2105714972","https://openalex.org/W2107728696","https://openalex.org/W2109553965","https://openalex.org/W2114998496","https://openalex.org/W2117557320","https://openalex.org/W2119340328","https://openalex.org/W2119362018","https://openalex.org/W2120772351","https://openalex.org/W2121828161","https://openalex.org/W2122035121","https://openalex.org/W2124662626","https://openalex.org/W2126466006","https://openalex.org/W2126924668","https://openalex.org/W2128731054","https://openalex.org/W2129706781","https://openalex.org/W2131164829","https://openalex.org/W2132046933","https://openalex.org/W2132081807","https://openalex.org/W2136659582","https://openalex.org/W2137356209","https://openalex.org/W2137640371","https://openalex.org/W2139401433","https://openalex.org/W2141411594","https://openalex.org/W2145983370","https://openalex.org/W2150882562","https://openalex.org/W2151804955","https://openalex.org/W2157483415","https://openalex.org/W2158714788","https://openalex.org/W2159820963","https://openalex.org/W2160515562","https://openalex.org/W2160845145","https://openalex.org/W2161043701","https://openalex.org/W2161159766","https://openalex.org/W2164700062","https://openalex.org/W2166268906","https://openalex.org/W2170157200","https://openalex.org/W2741340870","https://openalex.org/W2803927613","https://openalex.org/W6639282673","https://openalex.org/W6676552512","https://openalex.org/W6684319383"],"related_works":["https://openalex.org/W1472344963","https://openalex.org/W2051969447","https://openalex.org/W3093937951","https://openalex.org/W2111937814","https://openalex.org/W2181549235","https://openalex.org/W2003319012","https://openalex.org/W2078298125","https://openalex.org/W2055553856","https://openalex.org/W2026660542","https://openalex.org/W1968549100"],"abstract_inverted_index":{"MOTIVATION:":[0],"Predicting":[1],"RNA-RNA":[2,42,60,106,134],"interactions":[3,20,43,61,90,107],"is":[4,205],"essential":[5],"for":[6,16,185],"determining":[7],"the":[8,17,58,128,164,189],"function":[9],"of":[10,19,57,94,98,115,132,199],"putative":[11],"non-coding":[12],"RNAs.":[13,158],"Existing":[14],"methods":[15,29],"prediction":[18,165],"are":[21],"all":[22],"based":[23],"on":[24,110,177],"single":[25],"sequences.":[26,100],"Since":[27],"comparative":[28,171],"have":[30,62],"already":[31],"been":[32],"useful":[33],"in":[34,80],"RNA":[35,99,153],"structure":[36,137],"determination,":[37],"we":[38,50,139,161],"assume":[39,52],"that":[40,53,75,163],"conserved":[41,46],"also":[44,63],"imply":[45],"function.":[47],"Of":[48],"these,":[49],"further":[51],"a":[54,72,111,145],"non-negligible":[55],"amount":[56],"existing":[59],"acquired":[64],"compensating":[65],"base":[66,84],"changes":[67],"throughout":[68],"evolution.":[69],"We":[70,192],"implement":[71],"method,":[73],"PETcofold,":[74],"can":[76,166,211],"take":[77],"covariance":[78,186],"information":[79],"intra-molecular":[81],"and":[82,91,120,136,154,210],"inter-molecular":[83],"pairs":[85],"into":[86],"account":[87],"to":[88,104,142],"predict":[89,105],"secondary":[92],"structures":[93],"two":[95],"multiple":[96],"alignments":[97],"RESULTS:":[101],"PETcofold's":[102],"ability":[103],"was":[108,124,175],"evaluated":[109,176],"carefully":[112],"curated":[113],"dataset":[114],"32":[116],"bacterial":[117,156],"small":[118,151,157],"RNAs":[119],"their":[121],"targets,":[122],"which":[123],"manually":[125],"extracted":[126],"from":[127,214],"literature.":[129],"For":[130,159],"evaluation":[131],"both":[133],"interaction":[135,190],"prediction,":[138],"were":[140],"able":[141],"extract":[143],"only":[144],"few":[146],"high-quality":[147],"examples:":[148],"one":[149],"vertebrate":[150],"nucleolar":[152],"four":[155],"these":[160],"show":[162],"be":[167,212],"improved":[168],"by":[169],"our":[170],"approach.":[172],"Furthermore,":[173],"PETcofold":[174,204],"controlled":[178],"data":[179],"with":[180,196],"phylogenetically":[181],"simulated":[182],"sequences":[183],"enriched":[184],"patterns":[187],"at":[188],"sites.":[191],"observed":[193],"increased":[194,197],"performance":[195],"amounts":[198],"covariance.":[200],"AVAILABILITY:":[201],"The":[202],"program":[203],"available":[206],"as":[207],"source":[208],"code":[209],"downloaded":[213],"http://rth.dk/resources/petcofold.":[215]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":11}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
