{"id":"https://openalex.org/W2792896230","doi":"https://doi.org/10.1093/bioinformatics/bty158","title":"CMV: visualization for RNA and protein family models and their comparisons","display_name":"CMV: visualization for RNA and protein family models and their comparisons","publication_year":2018,"publication_date":"2018-03-15","ids":{"openalex":"https://openalex.org/W2792896230","doi":"https://doi.org/10.1093/bioinformatics/bty158","mag":"2792896230"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty158","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty158","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2676/25230863/bty158.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"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2676/25230863/bty158.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063976174","display_name":"Florian Eggenhofer","orcid":"https://orcid.org/0000-0001-9564-7525"},"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"]},{"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":["AT","DE"],"is_corresponding":true,"raw_author_name":"Florian Eggenhofer","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany","Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria"],"raw_orcid":"https://orcid.org/0000-0001-9564-7525","affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"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":["Bioinformatics and Computational Biology Research Group, University of Vienna, Vienna, Austria","Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biology Research Group, University of Vienna, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"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/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":"Rolf Backofen","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany","Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005332412","display_name":"Christian H\u00f6ner zu Siederdissen","orcid":"https://orcid.org/0000-0001-9517-5839"},"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"]},{"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":["AT","DE"],"is_corresponding":true,"raw_author_name":"Christian H\u00f6ner zu Siederdissen","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Leipzig, D-04107 Leipzig, Germany","Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria","Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Leipzig, D-04107 Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5005332412","https://openalex.org/A5063976174"],"corresponding_institution_ids":["https://openalex.org/I129774422","https://openalex.org/I161046081","https://openalex.org/I926574661"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":1430,"currency":"EUR","value_usd":1542},"fwci":1.2199,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.80664272,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"34","issue":"15","first_page":"2676","last_page":"2678"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11112","display_name":"Viral Infections and Immunology Research","score":0.9926999807357788,"subfield":{"id":"https://openalex.org/subfields/2705","display_name":"Cardiology and Cardiovascular Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11112","display_name":"Viral Infections and Immunology Research","score":0.9926999807357788,"subfield":{"id":"https://openalex.org/subfields/2705","display_name":"Cardiology and Cardiovascular Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10981","display_name":"Cytomegalovirus and herpesvirus research","score":0.9894999861717224,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12610","display_name":"RNA regulation and disease","score":0.9567000269889832,"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/visualization","display_name":"Visualization","score":0.6914603114128113},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5548247694969177},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.529870867729187},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5223580598831177},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30240598320961},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20557671785354614},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.19769561290740967},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07885748147964478}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6914603114128113},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5548247694969177},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.529870867729187},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5223580598831177},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30240598320961},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20557671785354614},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.19769561290740967},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07885748147964478}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty158","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty158","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2676/25230863/bty158.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":"pmh:oai:europepmc.org:5027416","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6061798","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty158","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty158","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/15/2676/25230863/bty158.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/G4246217526","display_name":null,"funder_award_id":"F 4305-B09","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"},{"id":"https://openalex.org/G7591315836","display_name":null,"funder_award_id":"BA 2168/3-3","funder_id":"https://openalex.org/F4320308022","funder_display_name":"California Department of Fish and Game"},{"id":"https://openalex.org/G8919312231","display_name":null,"funder_award_id":"BA 2168/16-1","funder_id":"https://openalex.org/F4320308022","funder_display_name":"California Department of Fish and Game"}],"funders":[{"id":"https://openalex.org/F4320308022","display_name":"California Department of Fish and Game","ror":"https://ror.org/02v6w2r95"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W2011271395","https://openalex.org/W2102122585","https://openalex.org/W2108230379","https://openalex.org/W2128976922","https://openalex.org/W2138122982","https://openalex.org/W2138631903","https://openalex.org/W2141152740","https://openalex.org/W2148419405","https://openalex.org/W2166706771","https://openalex.org/W2224056471","https://openalex.org/W2468840043","https://openalex.org/W2593813786","https://openalex.org/W2619630784","https://openalex.org/W2621270629","https://openalex.org/W2766848373","https://openalex.org/W2803724695","https://openalex.org/W2943934469","https://openalex.org/W2991913838"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189"],"abstract_inverted_index":{"Abstract":[0],"Summary":[1],"A":[2],"standard":[3],"method":[4],"for":[5],"the":[6,23,61,99],"identification":[7],"of":[8,25,63,89,111,117],"novel":[9],"RNAs":[10],"or":[11,35,80],"proteins":[12],"is":[13],"homology":[14],"search":[15],"via":[16],"probabilistic":[17],"models.":[18],"One":[19],"approach":[20],"relies":[21],"on":[22],"definition":[24],"families,":[26],"which":[27],"can":[28],"be":[29],"encoded":[30],"as":[31,68],"covariance":[32],"models":[33,67],"(CMs)":[34],"Hidden":[36],"Markov":[37],"Models":[38],"(HMMs).":[39],"While":[40],"being":[41],"powerful":[42],"tools,":[43],"their":[44,53],"complexity":[45],"makes":[46],"it":[47],"tedious":[48],"to":[49,60],"investigate":[50],"them":[51,95],"in":[52,69,96],"(default)":[54],"tabulated":[55],"form.":[56],"This":[57],"specifically":[58],"applies":[59],"interpretation":[62],"comparisons":[64,113],"between":[65],"multiple":[66],"family":[70],"clans.":[71],"The":[72],"Covariance":[73],"model":[74,112],"visualization":[75],"tools":[76],"(CMV)":[77],"visualize":[78],"CMs":[79],"HMMs":[81,90],"to:":[82],"I)":[83],"Obtain":[84],"an":[85],"easily":[86],"interpretable":[87],"representation":[88],"and":[91,114,120],"CMs;":[92],"II)":[93],"Put":[94],"context":[97],"with":[98],"structural":[100],"sequence":[101],"alignments":[102],"they":[103],"have":[104],"been":[105],"created":[106],"from;":[107],"III)":[108],"Investigate":[109],"results":[110],"highlight":[115],"regions":[116],"interest.":[118],"Availability":[119],"implementation":[121],"Source":[122],"code":[123],"(http://www.github.com/eggzilla/cmv),":[124],"web-service":[125],"(http://rna.informatik.uni-freiburg.de/CMVS).":[126],"Supplementary":[127,129],"information":[128],"data":[130],"are":[131],"available":[132],"at":[133],"Bioinformatics":[134],"online.":[135]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
