{"id":"https://openalex.org/W1993324010","doi":"https://doi.org/10.1093/nar/gkn278","title":"R-Coffee: a web server for accurately aligning noncoding RNA sequences","display_name":"R-Coffee: a web server for accurately aligning noncoding RNA sequences","publication_year":2008,"publication_date":"2008-05-15","ids":{"openalex":"https://openalex.org/W1993324010","doi":"https://doi.org/10.1093/nar/gkn278","mag":"1993324010","pmid":"https://pubmed.ncbi.nlm.nih.gov/18483080"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn278","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W10/7627355/gkn278.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/W10/7627355/gkn278.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039131441","display_name":"S\u00e9bastien Moretti","orcid":"https://orcid.org/0000-0003-3947-488X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"S. Moretti","raw_affiliation_strings":["Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036376802","display_name":"Andreas Wilm","orcid":"https://orcid.org/0000-0002-7344-3764"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]},{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"funder","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH","ES","IE"],"is_corresponding":false,"raw_author_name":"A. Wilm","raw_affiliation_strings":["Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland, 2 The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 3 Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain","SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland, 2 The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 3 Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210137962","https://openalex.org/I100930933"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090607558","display_name":"Desmond G. Higgins","orcid":"https://orcid.org/0000-0002-3952-3285"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]},{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"funder","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH","ES","IE"],"is_corresponding":false,"raw_author_name":"D. G. Higgins","raw_affiliation_strings":["Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland, 2 The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 3 Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain","SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland, 2 The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 3 Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210137962","https://openalex.org/I100930933"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065825020","display_name":"Ioannis X\u00e9narios","orcid":"https://orcid.org/0000-0002-3413-6841"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]},{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"funder","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH","ES","IE"],"is_corresponding":false,"raw_author_name":"I. Xenarios","raw_affiliation_strings":["Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland, 2 The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 3 Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain","SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland, 2 The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 3 Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210137962","https://openalex.org/I100930933"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058332830","display_name":"C\u00e9dric Notredame","orcid":"https://orcid.org/0000-0003-1461-0988"},"institutions":[{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"funder","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH","ES","IE"],"is_corresponding":false,"raw_author_name":"C. Notredame","raw_affiliation_strings":["Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland, 2 The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 3 Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain","SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Genopode, UNIL, CH-1015 Lausanne, Switzerland, 2 The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 3 Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210137962","https://openalex.org/I100930933"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5039131441"],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.4895,"has_fulltext":true,"cited_by_count":66,"citation_normalized_percentile":{"value":0.88877251,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"36","issue":"Web Server","first_page":"W10","last_page":"W13"},"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/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/T11482","display_name":"RNA modifications and cancer","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"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7355789542198181},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.696774959564209},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6152228713035583},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5488420724868774},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.538285493850708},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5103947520256042},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.4941461384296417},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.49295663833618164},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48447513580322266},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4792928099632263},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.419027715921402},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38154807686805725},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.339718759059906},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2465974986553192},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19269093871116638},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.16458553075790405},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.15010255575180054},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.11522907018661499},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10387948155403137}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7355789542198181},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.696774959564209},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6152228713035583},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5488420724868774},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.538285493850708},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5103947520256042},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.4941461384296417},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.49295663833618164},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48447513580322266},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4792928099632263},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.419027715921402},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38154807686805725},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.339718759059906},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2465974986553192},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19269093871116638},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.16458553075790405},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.15010255575180054},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.11522907018661499},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10387948155403137},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"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":"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":"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":"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":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":"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":6,"locations":[{"id":"doi:10.1093/nar/gkn278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn278","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W10/7627355/gkn278.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:18483080","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18483080","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:iris.unil.ch:iris/186356","is_oa":true,"landing_page_url":"https://iris.unil.ch/handle/iris/186356","pdf_url":"https://iris.unil.ch/bitstreams/923163c3-9e52-4e12-a07a-f26997c60192/download","source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:doc.rero.ch:294141","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400148","display_name":"reroDoc Digital Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:pubmedcentral.nih.gov:2447777","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2447777","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:serval.unil.ch:BIB_D39CC5C415A8","is_oa":true,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_D39CC5C415A8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, vol. 36, no. Web Server issue, pp. W10-W13","raw_type":"info:eu-repo/semantics/submittedVersion"}],"best_oa_location":{"id":"doi:10.1093/nar/gkn278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn278","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W10/7627355/gkn278.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/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1993324010.pdf","grobid_xml":"https://content.openalex.org/works/W1993324010.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1522740115","https://openalex.org/W1976361312","https://openalex.org/W2009736453","https://openalex.org/W2025305823","https://openalex.org/W2074231493","https://openalex.org/W2095145214","https://openalex.org/W2099383450","https://openalex.org/W2102502076","https://openalex.org/W2103250001","https://openalex.org/W2103899452","https://openalex.org/W2108187446","https://openalex.org/W2111773652","https://openalex.org/W2122035121","https://openalex.org/W2125038106","https://openalex.org/W2132926880","https://openalex.org/W2138369959","https://openalex.org/W2140872496","https://openalex.org/W2141157874","https://openalex.org/W2141670298","https://openalex.org/W2144362290","https://openalex.org/W2146416885","https://openalex.org/W2151994495","https://openalex.org/W2156563976","https://openalex.org/W2163798335","https://openalex.org/W2166745309","https://openalex.org/W2170157200","https://openalex.org/W2803927613"],"related_works":["https://openalex.org/W1975806245","https://openalex.org/W2345156963","https://openalex.org/W2187357871","https://openalex.org/W2135668486","https://openalex.org/W2144151678","https://openalex.org/W2105364679","https://openalex.org/W1996516710","https://openalex.org/W2039746015","https://openalex.org/W2055553856","https://openalex.org/W2167269469"],"abstract_inverted_index":{"The":[0,56,80,87,92,186],"R-Coffee":[1,20,31,110,133,187],"web":[2,188],"server":[3,88,189],"produces":[4],"highly":[5,62],"accurate":[6,115],"multiple":[7,43],"alignments":[8,67],"of":[9,53,138,168],"noncoding":[10],"RNA":[11,117,153],"(ncRNA)":[12],"sequences,":[13,176],"taking":[14],"into":[15],"account":[16],"predicted":[17,84],"secondary":[18,74,81],"structures.":[19],"uses":[21,40,132],"a":[22,50,113,123],"novel":[23],"algorithm":[24],"recently":[25],"incorporated":[26],"in":[27,69],"the":[28,34,66,70,73,78,136,139,144,163,169,178],"T-Coffee":[29],"package.":[30],"works":[32],"along":[33],"same":[35],"lines":[36],"as":[37],"T-Coffee:":[38],"it":[39],"pairwise":[41,116],"or":[42],"sequence":[44],"alignment":[45,118,172],"(MSA)":[46],"methods":[47,173],"to":[48,97,134,149],"compute":[49],"primary":[51],"library":[52,71],"input":[54],"alignments.":[55],"program":[57],"then":[58],"computes":[59],"an":[60],"MSA":[61],"consistent":[63],"with":[64,77,111],"both":[65],"contained":[68],"and":[72,108,156],"structures":[75,82],"associated":[76],"sequences.":[79,185],"are":[83],"using":[85],"RNAplfold.":[86],"provides":[89],"two":[90],"modes.":[91],"slow/accurate":[93],"mode":[94],"is":[95,166,190],"restricted":[96],"small":[98],"datasets":[99,122],"(less":[100],"than":[101,105],"5":[102],"sequences":[103],"less":[104],"150":[106],"nucleotides)":[107],"combines":[109,143],"Consan,":[112],"very":[114],"method.":[119],"For":[120],"larger":[121],"fast":[124],"method":[125],"can":[126],"be":[127],"used":[128],"(RM-Coffee":[129],"mode),":[130],"that":[131,162],"combine":[135],"output":[137],"three":[140],"packages":[141],"which":[142],"outputs":[145],"from":[146],"programs":[147],"found":[148],"perform":[150],"best":[151,170],"on":[152,183],"(MUSCLE,":[154],"MAFFT":[155],"ProbConsRNA).":[157],"Our":[158],"BRAliBase":[159],"benchmarks":[160],"indicate":[161],"R-Coffee/Consan":[164],"combination":[165],"one":[167],"ncRNA":[171],"for":[174],"short":[175],"while":[177],"RM-Coffee":[179],"gives":[180],"comparable":[181],"results":[182],"longer":[184],"available":[191],"at":[192],"http://www.tcoffee.org.":[193]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":9}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
