{"id":"https://openalex.org/W3100972074","doi":"https://doi.org/10.1186/s13015-020-00179-w","title":"Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains","display_name":"Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains","publication_year":2020,"publication_date":"2020-11-13","ids":{"openalex":"https://openalex.org/W3100972074","doi":"https://doi.org/10.1186/s13015-020-00179-w","mag":"3100972074","pmid":"https://pubmed.ncbi.nlm.nih.gov/33292340"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-020-00179-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-020-00179-w","pdf_url":null,"source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s13015-020-00179-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017381991","display_name":"Milad Miladi","orcid":"https://orcid.org/0000-0002-0173-3009"},"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":"Milad Miladi","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-0173-3009","affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016009812","display_name":"Martin Raden","orcid":"https://orcid.org/0000-0002-7926-5911"},"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":"Martin Raden","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103135268","display_name":"Sebastian Will","orcid":"https://orcid.org/0000-0002-2376-9205"},"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/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210145102","display_name":"Institut Polytechnique de Paris","ror":"https://ror.org/042tfbd02","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210145102"]}],"countries":["AT","FR"],"is_corresponding":false,"raw_author_name":"Sebastian Will","raw_affiliation_strings":["Bioinformatics group (AMIBIO), Laboratoire d'Informatique de l'\u00c9cole Polytechnique (LIX), Institut Polytechnique de Paris (IPP), Batiment Turing, 1 rue d'Estienne d'Orve, Palaiseau, France","Theoretical Biochemistry Group (TBI), Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics group (AMIBIO), Laboratoire d'Informatique de l'\u00c9cole Polytechnique (LIX), Institut Polytechnique de Paris (IPP), Batiment Turing, 1 rue d'Estienne d'Orve, Palaiseau, France","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I4210145102"]},{"raw_affiliation_string":"Theoretical Biochemistry Group (TBI), Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"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":false,"raw_author_name":"Rolf Backofen","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, Germany. backofen@informatik.uni-freiburg.de","Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Sch\u00e4nzlestr. 18, Freiburg, Germany. backofen@informatik.uni-freiburg.de","Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8231-3323","affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, Germany. backofen@informatik.uni-freiburg.de","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Sch\u00e4nzlestr. 18, Freiburg, Germany. backofen@informatik.uni-freiburg.de","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5017381991"],"corresponding_institution_ids":["https://openalex.org/I161046081"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1568,"currency":"EUR","value_usd":1691},"fwci":0.1667,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.51272453,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"15","issue":"1","first_page":"19","last_page":"19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9753999710083008,"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":0.9753999710083008,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.009600000455975533,"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":0.0019000000320374966,"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/computer-science","display_name":"Computer science","score":0.7687321901321411},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.6412903070449829},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.6251431703567505},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5576587319374084},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.48161810636520386},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.421808123588562},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39775633811950684},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1836947202682495},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.12125685811042786},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12105298042297363}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7687321901321411},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.6412903070449829},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6251431703567505},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5576587319374084},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.48161810636520386},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.421808123588562},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39775633811950684},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1836947202682495},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.12125685811042786},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12105298042297363},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13015-020-00179-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-020-00179-w","pdf_url":null,"source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:33292340","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33292340","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:HAL:hal-03131203v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03131203","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"Algorithms for Molecular Biology, 2020, 15 (1), &#x27E8;10.1186/s13015-020-00179-w&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:4343f3e9ac3a4ca7be8b6fa4b6050507","is_oa":true,"landing_page_url":"https://doaj.org/article/4343f3e9ac3a4ca7be8b6fa4b6050507","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-11 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7666477","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7666477","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-020-00179-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-020-00179-w","pdf_url":null,"source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8299999833106995,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2201129563","display_name":null,"funder_award_id":"BA2168/3-3","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6994766618","display_name":null,"funder_award_id":"CIBSS-EXC-2189-Project ID 390939984","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7566894236","display_name":null,"funder_award_id":"BA2168/16-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8245574974","display_name":null,"funder_award_id":"BA2168/21-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W166206240","https://openalex.org/W1522740115","https://openalex.org/W1861164398","https://openalex.org/W1975148447","https://openalex.org/W1984675364","https://openalex.org/W2009818318","https://openalex.org/W2014914391","https://openalex.org/W2018216725","https://openalex.org/W2068205741","https://openalex.org/W2095145214","https://openalex.org/W2103899452","https://openalex.org/W2111773652","https://openalex.org/W2115215562","https://openalex.org/W2117431427","https://openalex.org/W2122035121","https://openalex.org/W2133279153","https://openalex.org/W2137356209","https://openalex.org/W2139541234","https://openalex.org/W2147394603","https://openalex.org/W2163798335","https://openalex.org/W2166745309","https://openalex.org/W2170157200","https://openalex.org/W2259311060","https://openalex.org/W2593813786","https://openalex.org/W2803927613","https://openalex.org/W2951298881"],"related_works":["https://openalex.org/W2943623134","https://openalex.org/W1660242800","https://openalex.org/W2494523064","https://openalex.org/W2215759665","https://openalex.org/W2960358116","https://openalex.org/W2077211377","https://openalex.org/W1497573972","https://openalex.org/W2071659383","https://openalex.org/W1846253165","https://openalex.org/W2124122503"],"abstract_inverted_index":{"MOTIVATION:":[0],"Simultaneous":[1],"alignment":[2,164],"and":[3,20,54,155,165,202,207],"folding":[4,166,205],"(SA&F)":[5],"of":[6,17,38,56,87,94,112,119,167,179,190],"RNAs":[7,19,168],"is":[8,208],"the":[9,15,31,43,48,57,77,92,99,110,113,153,177,185,191],"indispensable":[10],"gold":[11],"standard":[12],"for":[13],"inferring":[14],"structure":[16,141],"non-coding":[18],"their":[21],"general":[22],"analysis.":[23],"The":[24],"original":[25],"algorithm,":[26],"proposed":[27,62],"by":[28,68,170],"Sankoff,":[29],"solves":[30],"theoretical":[32],"problem":[33],"exactly":[34],"with":[35,109],"a":[36,84,104,145],"complexity":[37,67],"[Formula:":[39],"see":[40],"text]":[41],"in":[42,204],"full":[44,100,115],"energy":[45,71,101,116,188],"model.":[46,117],"Over":[47],"last":[49],"two":[50],"decades,":[51],"several":[52],"variants":[53],"improvements":[55],"Sankoff":[58],"algorithm":[59,89,159],"have":[60],"been":[61],"to":[63,103,138,152],"reduce":[64],"its":[65,199],"extreme":[66],"proposing":[69],"simplified":[70],"models":[72],"or":[73],"imposing":[74],"restrictions":[75],"on":[76],"predicted":[78],"alignments.":[79],"RESULTS:":[80],"Here,":[81],"we":[82],"introduce":[83],"novel":[85,158],"variant":[86],"Sankoff's":[88,192],"that":[90,136,196],"reconciles":[91],"simplifications":[93],"PMcomp,":[95],"namely":[96],"moving":[97],"from":[98,122,131,176],"model":[102,128,149,189],"simpler":[105],"base":[106,124,133],"pair-based":[107],"model,":[108],"accuracy":[111],"loop-based":[114,186],"Instead":[118],"estimating":[120],"pseudo-energies":[121],"unconditional":[123],"pair":[125,134],"probabilities,":[126,142],"our":[127],"calculates":[129],"energies":[130],"conditional":[132,146],"probabilities":[135],"allow":[137],"accurately":[139],"capture":[140],"which":[143],"obey":[144],"dependency.":[147],"This":[148],"gives":[150],"rise":[151],"fast":[154],"highly":[156],"accurate":[157],"Pankov":[160,174,197],"(Probabilistic":[161],"Sankoff-like":[162],"simultaneous":[163],"inspired":[169],"Markov":[171],"chains).":[172],"CONCLUSIONS:":[173],"benefits":[175],"speed-up":[178],"excluding":[180],"unreliable":[181],"base-pairing":[182],"without":[183],"compromising":[184],"free":[187],"algorithm.":[193],"We":[194],"show":[195],"outperforms":[198],"predecessors":[200],"LocARNA":[201],"SPARSE":[203],"quality":[206],"faster":[209],"than":[210],"LocARNA.":[211]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-30T09:04:40.226872","created_date":"2025-10-10T00:00:00"}
