{"id":"https://openalex.org/W7225619310","doi":"https://doi.org/10.64898/2026.11.06.764809","title":"LinearKnot: linear-time ensemble analysis of RNA density-2 pseudoknots under hierarchical folding","display_name":"LinearKnot: linear-time ensemble analysis of RNA density-2 pseudoknots under hierarchical folding","publication_year":2026,"publication_date":"2026-11-09","ids":{"openalex":"https://openalex.org/W7225619310","doi":"https://doi.org/10.64898/2026.11.06.764809"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.06.764809","doi":"https://doi.org/10.64898/2026.11.06.764809","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764809","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764809.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764809.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5120114018","display_name":"Takumi Otagaki","orcid":"https://orcid.org/0009-0004-7123-9585","observed_orcids":["https://orcid.org/0009-0004-7123-9585"]},"institutions":[{"id":"https://openalex.org/I4400009020","display_name":"Institute of Science Tokyo","ror":"https://ror.org/05dqf9946","country_code":"JP","type":"education","lineage":["https://openalex.org/I4400009020"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takumi Otagaki","raw_affiliation_strings":["Institute of Science Tokyo"],"raw_orcid":"https://orcid.org/0009-0004-7123-9585","affiliations":[{"raw_affiliation_string":"Institute of Science Tokyo","institution_ids":["https://openalex.org/I4400009020"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076175043","display_name":"Kengo Sato","orcid":"https://orcid.org/0000-0001-6744-7390","observed_orcids":["https://orcid.org/0000-0001-6744-7390"]},"institutions":[{"id":"https://openalex.org/I4400009020","display_name":"Institute of Science Tokyo","ror":"https://ror.org/05dqf9946","country_code":"JP","type":"education","lineage":["https://openalex.org/I4400009020"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kengo Sato","raw_affiliation_strings":["Institute of Science Tokyo"],"raw_orcid":"https://orcid.org/0000-0001-6744-7390","affiliations":[{"raw_affiliation_string":"Institute of Science Tokyo","institution_ids":["https://openalex.org/I4400009020"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5076175043"],"corresponding_institution_ids":["https://openalex.org/I4400009020"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9984999895095825,"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":0.9984999895095825,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.00019999999494757503,"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/T10604","display_name":"RNA Research and Splicing","score":0.00019999999494757503,"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/rna-pseudoknots","display_name":"RNA pseudoknots","score":0.9179999828338623},{"id":"https://openalex.org/keywords/hierarchical-folding","display_name":"hierarchical folding","score":0.6489999890327454},{"id":"https://openalex.org/keywords/linear-time-algorithms","display_name":"linear-time algorithms","score":0.5770000219345093},{"id":"https://openalex.org/keywords/partition-function","display_name":"partition function","score":0.6949999928474426},{"id":"https://openalex.org/keywords/minimum-free-energy","display_name":"minimum free energy","score":0.8320000171661377},{"id":"https://openalex.org/keywords/base-pairing-probability","display_name":"base pairing probability","score":0.8320000171661377},{"id":"https://openalex.org/keywords/long-non-coding-rna","display_name":"long non-coding RNA","score":0.8669999837875366},{"id":"https://openalex.org/keywords/rna-structure-prediction","display_name":"RNA structure prediction","score":0.5210000276565552},{"id":"https://openalex.org/keywords/structural-context","display_name":"structural context","score":0.32499998807907104},{"id":"https://openalex.org/keywords/unpaired-bases","display_name":"unpaired bases","score":0.4189999997615814},{"id":"https://openalex.org/keywords/memory-efficiency","display_name":"memory efficiency","score":0.32600000500679016}],"concepts":[{"id":"https://openalex.org/C14103023","wikidata":"https://www.wikidata.org/wiki/Q11681459","display_name":"Pairing","level":3,"score":0.6503000259399414},{"id":"https://openalex.org/C42812","wikidata":"https://www.wikidata.org/wiki/Q1082910","display_name":"Partition (number theory)","level":2,"score":0.5788000226020813},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.5690000057220459},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5184999704360962},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.5144000053405762},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.47290000319480896},{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.450300008058548},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.4397999942302704},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.439300000667572},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42239999771118164},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3303999900817871},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.32989999651908875},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.31540000438690186},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.30820000171661377},{"id":"https://openalex.org/C178635117","wikidata":"https://www.wikidata.org/wiki/Q747499","display_name":"RADIUS","level":2,"score":0.305400013923645},{"id":"https://openalex.org/C21308566","wikidata":"https://www.wikidata.org/wiki/Q7169365","display_name":"Permutation (music)","level":2,"score":0.296099990606308},{"id":"https://openalex.org/C2778751112","wikidata":"https://www.wikidata.org/wiki/Q835016","display_name":"Window (computing)","level":2,"score":0.29409998655319214},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.29249998927116394},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.27549999952316284},{"id":"https://openalex.org/C99611785","wikidata":"https://www.wikidata.org/wiki/Q6453233","display_name":"Duplex (building)","level":3,"score":0.2718000113964081},{"id":"https://openalex.org/C2778401447","wikidata":"https://www.wikidata.org/wiki/Q7140637","display_name":"Partition function (quantum field theory)","level":2,"score":0.2565999925136566}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.06.764809","doi":"https://doi.org/10.64898/2026.11.06.764809","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764809","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764809.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.06.764809","doi":"https://doi.org/10.64898/2026.11.06.764809","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764809","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764809.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225619310.pdf","grobid_xml":"https://content.openalex.org/works/W7225619310.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4405596815","https://openalex.org/W7204477832","https://openalex.org/W3043664941","https://openalex.org/W2807635396","https://openalex.org/W3201863879","https://openalex.org/W2141351700","https://openalex.org/W7098923808","https://openalex.org/W1805148049","https://openalex.org/W7155192359","https://openalex.org/W2997483194"],"abstract_inverted_index":{"Motivation:":[0],"A":[1,289],"pseudoknot":[2,280],"is":[3,37,112,118],"an":[4],"arrangement":[5],"of":[6,160,286],"crossing":[7,107],"base":[8],"pairs.":[9],"Pseudoknots":[10],"complicate":[11],"structure":[12,23,33],"prediction":[13],"and":[14,59,71,80,99,135,141,171,201,217,227,234,238,245,267,299,310,321],"calculations":[15,219,260],"over":[16,128,148],"possible":[17],"structures":[18,55,83],"(an":[19],"ensemble).":[20],"CParty":[21,45,193],"sums":[22],"weights":[24],"for":[25,97,169,173,182,261],"hierarchical":[26],"pseudoknots":[27],"that":[28,115],"keep":[29],"a":[30,116,274,279,287,305],"supplied":[31],"pseudoknot-free":[32,290],"(scaffold).":[34],"Its":[35],"time":[36,89],"cubic":[38],"in":[39,56,90,151,242,304],"sequence":[40,91],"length.":[41,92],"Results:":[42],"LinearKnot":[43,178,312],"approximates":[44],"with":[46,138,292],"beam":[47,66,243],"pruning.":[48],"It":[49],"combines":[50],"at":[51,220,253,317,324],"most":[52],"two":[53],"partial":[54],"each":[57,121,125,240],"step":[58],"keeps":[60],"the":[61,113,132,152,157,207,259,293,301,314],"highest-ranked":[62],"candidates.":[63],"At":[64,154,175,256],"fixed":[65],"width,":[67],"hairpin":[68,306],"length":[69],"limit,":[70,74],"scaffold":[72,295],"search":[73],"partition":[75,180],"functions,":[76],"minimum-free-energy":[77],"(MFE)":[78],"predictions,":[79],"representative":[81],"\u03b3-centroid":[82],"from":[84],"base-pairing":[85],"probabilities":[86,96,140,236],"take":[87],"linear":[88],"Loop":[93],"profiles":[94],"give":[95],"pairing":[98,129,170,235],"six":[100],"unpaired":[101,133,150,283],"loop":[102],"types,":[103],"including":[104],"gaps":[105],"between":[106],"stems":[108],"(PseudoLoop).":[109],"Window":[110],"accessibility":[111,298],"probability":[114],"window":[117,276,302],"unpaired.":[119,308],"For":[120,206],"RNA,":[122,273],"we":[123],"compared":[124,231],"base's":[126],"distributions":[127],"partners":[130],"(including":[131],"state)":[134],"structural":[136],"contexts":[137],"exact":[139],"averaged":[142],"their":[143],"total":[144],"variation":[145],"(TV)":[146],"distances":[147],"bases":[149],"scaffold.":[153],"width":[155,176,221,244,257],"200,":[156,258],"90th":[158],"percentiles":[159],"these":[161],"RNA":[162,211],"averages":[163],"among":[164],"300-399-base":[165],"RNAs":[166,186,195],"were":[167],"0.0015":[168],"0.0017":[172],"contexts.":[174],"100,":[177],"completed":[179,194],"functions":[181],"all":[183],"107":[184],"real":[185],"through":[187],"29":[188],"kilobases.":[189],"Under":[190],"our":[191],"settings,":[192],"up":[196],"to":[197,278],"about":[198,224,264],"1":[199],"kilobase":[200],"was":[202,281],"faster":[203],"on":[204],"them.":[205],"RNAcentral":[208],"long":[209],"non-coding":[210],"URS00023A4DB9":[212,262],"(29,106":[213],"nt),":[214],"partition-function,":[215],"pairing-probability,":[216],"MFE":[218],"100":[222],"took":[223,263],"7":[225],"minutes":[226,266],"3.22":[228],"GiB.":[229,269],"We":[230],"free":[232],"energy":[233],"before":[237],"after":[239],"increase":[241],"local":[246],"limits.":[247],"These":[248],"changes":[249],"generally":[250],"became":[251],"smaller":[252],"larger":[254],"widths.":[255],"20":[265],"5.68":[268],"In":[270],"rat":[271],"telomerase":[272],"four-base":[275],"next":[277],"mostly":[282],"as":[284],"part":[285],"PseudoLoop.":[288],"calculation":[291],"same":[294],"gave":[296],"lower":[297],"placed":[300],"mainly":[303],"when":[307],"Availability":[309],"implementation:":[311],"provides":[313],"linearknot":[315],"command":[316],"https://github.com/TakumiOtagaki/LinearKnot.":[318],"Experiment":[319],"scripts":[320],"data":[322],"are":[323],"https://github.com/TakumiOtagaki/LinearKnotExperiments.":[325]},"counts_by_year":[],"updated_date":"2026-11-11T12:16:26.678958","created_date":"2026-11-10T00:00:00"}
