{"id":"https://openalex.org/W2981008535","doi":"https://doi.org/10.1142/s0219720019500318","title":"RNAknot: A new algorithm for RNA secondary structure prediction based on genetic algorithm and GRASP method","display_name":"RNAknot: A new algorithm for RNA secondary structure prediction based on genetic algorithm and GRASP method","publication_year":2019,"publication_date":"2019-10-01","ids":{"openalex":"https://openalex.org/W2981008535","doi":"https://doi.org/10.1142/s0219720019500318","mag":"2981008535","pmid":"https://pubmed.ncbi.nlm.nih.gov/31856666"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720019500318","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500318","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050319481","display_name":"Abdelhakim El Fatmi","orcid":"https://orcid.org/0000-0003-2641-2399"},"institutions":[{"id":"https://openalex.org/I4210153608","display_name":"Universit\u00e9 Moulay Ismail de Meknes","ror":"https://ror.org/04cnscd67","country_code":"MA","type":"education","lineage":["https://openalex.org/I4210153608"]}],"countries":["MA"],"is_corresponding":true,"raw_author_name":"Abdelhakim El Fatmi","raw_affiliation_strings":["Computer Science Department, MACS Lab, Faculty of Science, Moulay Ismail University, Meknes, BP 11201, Morocco"],"raw_orcid":"https://orcid.org/0000-0003-2641-2399","affiliations":[{"raw_affiliation_string":"Computer Science Department, MACS Lab, Faculty of Science, Moulay Ismail University, Meknes, BP 11201, Morocco","institution_ids":["https://openalex.org/I4210153608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010670241","display_name":"M. Ali Bekri","orcid":"https://orcid.org/0009-0004-1296-5624"},"institutions":[{"id":"https://openalex.org/I4210153608","display_name":"Universit\u00e9 Moulay Ismail de Meknes","ror":"https://ror.org/04cnscd67","country_code":"MA","type":"education","lineage":["https://openalex.org/I4210153608"]}],"countries":["MA"],"is_corresponding":false,"raw_author_name":"M. Ali Bekri","raw_affiliation_strings":["Computer Science Department, MACS Lab, Faculty of Science, Moulay Ismail University, Meknes, BP 11201, Morocco"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, MACS Lab, Faculty of Science, Moulay Ismail University, Meknes, BP 11201, Morocco","institution_ids":["https://openalex.org/I4210153608"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043489542","display_name":"Said Benhlima","orcid":"https://orcid.org/0000-0002-8445-9470"},"institutions":[{"id":"https://openalex.org/I4210153608","display_name":"Universit\u00e9 Moulay Ismail de Meknes","ror":"https://ror.org/04cnscd67","country_code":"MA","type":"education","lineage":["https://openalex.org/I4210153608"]}],"countries":["MA"],"is_corresponding":false,"raw_author_name":"Said Benhlima","raw_affiliation_strings":["Computer Science Department, MACS Lab, Faculty of Science, Moulay Ismail University, Meknes, BP 11201, Morocco"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, MACS Lab, Faculty of Science, Moulay Ismail University, Meknes, BP 11201, Morocco","institution_ids":["https://openalex.org/I4210153608"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5050319481"],"corresponding_institution_ids":["https://openalex.org/I4210153608"],"apc_list":null,"apc_paid":null,"fwci":0.4295,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.62870837,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"17","issue":"05","first_page":"1950031","last_page":"1950031"},"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.994700014591217,"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":0.9941999912261963,"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/pseudoknot","display_name":"Pseudoknot","score":0.9490229487419128},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.7841095924377441},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.7351353764533997},{"id":"https://openalex.org/keywords/grasp","display_name":"GRASP","score":0.6092317700386047},{"id":"https://openalex.org/keywords/greedy-randomized-adaptive-search-procedure","display_name":"Greedy randomized adaptive search procedure","score":0.6010947227478027},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.5828421115875244},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5586538314819336},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4811219274997711},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4608215391635895},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.45294469594955444},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.41211119294166565},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.35828685760498047},{"id":"https://openalex.org/keywords/greedy-algorithm","display_name":"Greedy algorithm","score":0.3522289991378784},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3433976471424103},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24425789713859558},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.20389044284820557},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14523714780807495},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13736411929130554},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09845715761184692}],"concepts":[{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.9490229487419128},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.7841095924377441},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.7351353764533997},{"id":"https://openalex.org/C171268870","wikidata":"https://www.wikidata.org/wiki/Q1486676","display_name":"GRASP","level":2,"score":0.6092317700386047},{"id":"https://openalex.org/C126221529","wikidata":"https://www.wikidata.org/wiki/Q3116070","display_name":"Greedy randomized adaptive search procedure","level":3,"score":0.6010947227478027},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5828421115875244},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5586538314819336},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4811219274997711},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4608215391635895},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.45294469594955444},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.41211119294166565},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.35828685760498047},{"id":"https://openalex.org/C51823790","wikidata":"https://www.wikidata.org/wiki/Q504353","display_name":"Greedy algorithm","level":2,"score":0.3522289991378784},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3433976471424103},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24425789713859558},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.20389044284820557},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14523714780807495},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13736411929130554},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09845715761184692},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720019500318","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500318","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:31856666","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31856666","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.8100000023841858,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1543796220","https://openalex.org/W1583489351","https://openalex.org/W1725615870","https://openalex.org/W1966833356","https://openalex.org/W2001309107","https://openalex.org/W2004945910","https://openalex.org/W2009215595","https://openalex.org/W2009818318","https://openalex.org/W2020693276","https://openalex.org/W2054931730","https://openalex.org/W2056742043","https://openalex.org/W2065735339","https://openalex.org/W2076347392","https://openalex.org/W2080099035","https://openalex.org/W2102934142","https://openalex.org/W2104611815","https://openalex.org/W2106293441","https://openalex.org/W2117879815","https://openalex.org/W2118044280","https://openalex.org/W2134489577","https://openalex.org/W2136288913","https://openalex.org/W2141157874","https://openalex.org/W2146416885","https://openalex.org/W2162224067","https://openalex.org/W2548316818","https://openalex.org/W2997776631"],"related_works":["https://openalex.org/W2277088917","https://openalex.org/W4280543056","https://openalex.org/W2159621058","https://openalex.org/W2154172459","https://openalex.org/W2036643266","https://openalex.org/W1966171024","https://openalex.org/W4225160382","https://openalex.org/W2981008535","https://openalex.org/W2059090778","https://openalex.org/W2039746015"],"abstract_inverted_index":{"The":[0,181,204,280],"prediction":[1,193,213],"of":[2,27,62,70,109,150,162,188,206,215,269],"the":[3,25,89,133,141,148,151,173,212,227,231,236,248,252,255,262,266,277,289],"optimal":[4],"secondary":[5,52,85,191,257],"structure":[6,53,86,192,258],"for":[7,82],"a":[8,13,33,60,79,120,285],"given":[9],"RNA":[10,51,84,166,190,256],"sequence":[11],"represents":[12],"challenging":[14],"computational":[15],"problem":[16],"in":[17,40,68,104,288],"bioinformatics.":[18],"This":[19],"challenge":[20],"becomes":[21],"harder":[22],"especially":[23],"with":[24,54,186],"discovery":[26],"different":[28],"pseudoknot":[29,56,112],"classes,":[30,57],"which":[31,168],"is":[32,117,219,282],"complex":[34],"topology":[35],"that":[36,87,211],"plays":[37],"diverse":[38],"roles":[39],"biological":[41],"processes.":[42],"Many":[43],"recent":[44],"studies":[45],"have":[46,64,156,169],"been":[47,157,170],"proposed":[48,217],"to":[49,106,139,146,223,247,265,276],"predict":[50],"some":[55,189],"but":[58],"only":[59],"few":[61],"them":[63],"reached":[65],"satisfying":[66],"results":[67,183,205],"terms":[69],"both":[71],"complexity":[72],"and":[73,101,113,123,130,164,178,202,241,272],"accuracy.":[74],"Here":[75],"we":[76],"present":[77],"RNAknot,":[78],"new":[80],"method":[81,153],"predicting":[83],"contains":[88],"following":[90],"components:":[91],"stems,":[92],"hairpin":[93],"loops,":[94,100,103],"multi-branched":[95],"loops":[96],"or":[97],"multi-loops,":[98],"bulge":[99],"internal":[102],"addition":[105],"two":[107,160,174],"types":[108],"pseudoknots,":[110],"H-type":[111],"Hairpin":[114],"kissing.":[115],"RNAknot":[116,234,263],"based":[118],"on":[119],"genetic":[121],"algorithm":[122],"Greedy":[124],"Randomized":[125],"Adaptive":[126],"Search":[127],"Procedure":[128],"(GRASP),":[129],"it":[131],"uses":[132],"free":[134],"energy":[135],"as":[136,196,284],"fitness":[137],"function":[138],"evaluate":[140],"obtained":[142,182,225,260],"structures.":[143],"In":[144],"order":[145],"validate":[147],"performance":[149],"presented":[152],"131":[154],"tests":[155],"performed":[158],"using":[159],"datasets":[161],"26":[163],"105":[165],"sequences,":[167],"taken":[171],"from":[172],"data":[175],"bases":[176],"RNAstrand":[177],"Pseudobase":[179],"respectively.":[180],"are":[184],"compared":[185,222,246,275],"those":[187,224],"programs":[194],"such":[195],"Vs_subopt,":[197],"CyloFold,":[198],"IPknot,":[199],"Kinefold,":[200],"RNAstructure,":[201],"Sfold.":[203],"this":[207],"comparative":[208],"study":[209],"show":[210],"accuracy":[214],"our":[216],"approach":[218],"significantly":[220],"improved":[221],"by":[226,261],"other":[228,249,278],"programs.":[229,250,279],"For":[230],"first":[232],"dataset,":[233,254],"has":[235],"highest":[237,267],"specificity":[238],"(SP)":[239],"(71.23%)":[240],"sensitivity":[242],"(SN)":[243],"(72.15%)":[244],"averages":[245,268],"Concerning":[251],"second":[253],"predictions":[259],"correspond":[264],"SP":[270],"(85.49%)":[271],"F-measure":[273],"(79.97%)":[274],"program":[281],"available":[283],"jar":[286],"file":[287],"link:":[290],"www.bachmek.umi.ac.ma/wp-content/uploads/RNAknot.0.0.2.rar.":[291]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}