{"id":"https://openalex.org/W2164618041","doi":"https://doi.org/10.1109/cibcb.2007.4221229","title":"SARNA-Predict: A Study of RNA Secondary Structure Prediction Using Different Annealing Schedules","display_name":"SARNA-Predict: A Study of RNA Secondary Structure Prediction Using Different Annealing Schedules","publication_year":2007,"publication_date":"2007-04-01","ids":{"openalex":"https://openalex.org/W2164618041","doi":"https://doi.org/10.1109/cibcb.2007.4221229","mag":"2164618041"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2007.4221229","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2007.4221229","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5049705327","display_name":"Herbert H. Tsang","orcid":"https://orcid.org/0000-0001-8928-7375"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Herbert H. Tsang","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Surrey, BC, Canada"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Surrey, BC, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049270004","display_name":"Kay C. Wiese","orcid":"https://orcid.org/0000-0003-4507-1892"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Kay C. Wiese","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Surrey, BC, Canada"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Surrey, BC, Canada","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5049705327"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":null,"apc_paid":null,"fwci":1.6132,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.83020006,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"239","last_page":"246"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9966999888420105,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9915000200271606,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/simulated-annealing","display_name":"Simulated annealing","score":0.5939715504646301},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5880191326141357},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5161186456680298},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5002906322479248},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.48977136611938477},{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.461472749710083},{"id":"https://openalex.org/keywords/intron","display_name":"Intron","score":0.44879403710365295},{"id":"https://openalex.org/keywords/energy-minimization","display_name":"Energy minimization","score":0.43472400307655334},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3511439561843872},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.29576897621154785},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.14445185661315918},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1300470232963562},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11726602911949158}],"concepts":[{"id":"https://openalex.org/C126980161","wikidata":"https://www.wikidata.org/wiki/Q863783","display_name":"Simulated annealing","level":2,"score":0.5939715504646301},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5880191326141357},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5161186456680298},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5002906322479248},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.48977136611938477},{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.461472749710083},{"id":"https://openalex.org/C94671646","wikidata":"https://www.wikidata.org/wiki/Q207551","display_name":"Intron","level":3,"score":0.44879403710365295},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.43472400307655334},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3511439561843872},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.29576897621154785},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.14445185661315918},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1300470232963562},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11726602911949158},{"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/cibcb.2007.4221229","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2007.4221229","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.129.9426","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.129.9426","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.sfu.ca/~hhtsang/personal/papers/2007_CIBCB_TsangWiese.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8999999761581421}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W129209152","https://openalex.org/W569835445","https://openalex.org/W1479913101","https://openalex.org/W1509099686","https://openalex.org/W1512383952","https://openalex.org/W1945034450","https://openalex.org/W1982647060","https://openalex.org/W1988884185","https://openalex.org/W1990476811","https://openalex.org/W1996816381","https://openalex.org/W2005228957","https://openalex.org/W2017302704","https://openalex.org/W2017965868","https://openalex.org/W2020999234","https://openalex.org/W2021730381","https://openalex.org/W2024060531","https://openalex.org/W2025763720","https://openalex.org/W2028574527","https://openalex.org/W2046948610","https://openalex.org/W2048796447","https://openalex.org/W2049906941","https://openalex.org/W2051713039","https://openalex.org/W2056760934","https://openalex.org/W2075702353","https://openalex.org/W2079645034","https://openalex.org/W2097654784","https://openalex.org/W2098553089","https://openalex.org/W2107432340","https://openalex.org/W2128160420","https://openalex.org/W2131281445","https://openalex.org/W2140302584","https://openalex.org/W2141157874","https://openalex.org/W2142056356","https://openalex.org/W2144031478"],"related_works":["https://openalex.org/W2375684291","https://openalex.org/W2354676191","https://openalex.org/W2132461435","https://openalex.org/W1992534732","https://openalex.org/W2091418430","https://openalex.org/W2153731865","https://openalex.org/W2471196694","https://openalex.org/W2127982566","https://openalex.org/W2396713240","https://openalex.org/W2904092608"],"abstract_inverted_index":{"This":[0],"paper":[1,90],"presents":[2],"an":[3],"algorithm":[4,62,116,133,147,217,230],"for":[5,42,65,80,97,149,177,212],"RNA":[6,98,156,178],"secondary":[7,99],"structure":[8,67,100,225],"prediction":[9,137],"based":[10],"on":[11,54],"simulated":[12],"annealing":[13,25,121],"(SA)":[14],"and":[15,41,101,119,170,236],"also":[16],"studies":[17],"the":[18,50,66,75,92,102,111,115,128,131,144,184,190,200,222],"effect":[19],"of":[20,24,38,88,94,110,114,127,130,136,193,221],"using":[21],"different":[22,36],"types":[23,37],"schedules.":[26],"SA":[27,61],"is":[28,117,139,203,210,226],"known":[29,152],"to":[30,45,74,182,197,218],"be":[31,198],"effective":[32],"in":[33,49,134],"solving":[34],"many":[35],"minimization":[39,57],"problems":[40],"being":[43],"able":[44],"approximate":[46],"global":[47],"minima":[48],"solution":[51],"space.":[52],"Based":[53],"free":[55,70,77],"energy":[56,71,78],"techniques,":[58],"this":[59,89,194],"permutation-based":[60,95],"heuristically":[63],"searches":[64],"with":[68,143,234],"a":[69,107,213,238],"value":[72],"close":[73],"minimum":[76],"DeltaG":[79],"that":[81,199],"strand,":[82],"within":[83,206],"given":[84],"constraints.":[85],"Other":[86],"contributions":[87],"include":[91],"use":[93],"encoding":[96],"swap":[103],"mutation":[104],"operator.":[105],"Also,":[106],"detailed":[108],"study":[109],"convergence":[112],"behavior":[113],"conducted":[118],"various":[120],"schedules":[122],"are":[123,180],"investigated.":[124],"An":[125],"evaluation":[126],"performance":[129],"new":[132,229],"terms":[135],"accuracy":[138],"made":[140],"via":[141],"comparison":[142],"dynamic":[145,174],"programming":[146,175],"mfold":[148,235],"thirteen":[150],"individual":[151],"structures":[153],"from":[154],"four":[155],"classes":[157],"(5S":[158],"rRNA,":[159,164],"Group":[160,165],"I":[161,166],"intron":[162,167],"23":[163],"16S":[168,171],"rRNA":[169],"rRNA).":[172],"Although":[173],"algorithms":[176],"folding":[179,216],"guaranteed":[181],"give":[183],"mathematically":[185],"optimal":[186],"(minimum":[187],"energy)":[188],"structure,":[189],"fundamental":[191],"problem":[192],"approach":[195],"seems":[196],"thermodynamic":[201],"model":[202],"only":[204],"accurate":[205],"5-10%.":[207],"Therefore,":[208],"it":[209],"difficult":[211],"single":[214],"sequence":[215],"resolve":[219],"which":[220],"plausible":[223],"lowest-energy":[224],"correct.":[227],"The":[228],"showed":[231],"comparable":[232],"results":[233],"demonstrated":[237],"slightly":[239],"higher":[240],"specificity":[241]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
