{"id":"https://openalex.org/W2268094462","doi":"https://doi.org/10.1093/bioinformatics/btv748","title":"Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment","display_name":"Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment","publication_year":2015,"publication_date":"2015-12-24","ids":{"openalex":"https://openalex.org/W2268094462","doi":"https://doi.org/10.1093/bioinformatics/btv748","mag":"2268094462","pmid":"https://pubmed.ncbi.nlm.nih.gov/26704597"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv748","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv748","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1238/49018410/bioinformatics_32_8_1238.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","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1238/49018410/bioinformatics_32_8_1238.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025518020","display_name":"D. Sundfeld","orcid":"https://orcid.org/0000-0002-5147-3698"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR","DK"],"is_corresponding":false,"raw_author_name":"Daniel Sundfeld","raw_affiliation_strings":["1 Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and","2 Department of Computer Science, University of Brasilia, Bras\u00edlia, DF, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"2 Department of Computer Science, University of Brasilia, Bras\u00edlia, DF, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019722014","display_name":"Jakob H. Havgaard","orcid":"https://orcid.org/0000-0002-4816-814X"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jakob H. Havgaard","raw_affiliation_strings":["1 Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005717412","display_name":"Alba Cristina Magalh\u00e3es Alves de Melo","orcid":"https://orcid.org/0000-0001-5191-5209"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alba C. M. A. de Melo","raw_affiliation_strings":["2 Department of Computer Science, University of Brasilia, Bras\u00edlia, DF, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Computer Science, University of Brasilia, Bras\u00edlia, DF, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004614832","display_name":"Jan Gorodkin","orcid":"https://orcid.org/0000-0001-5823-4000"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Jan Gorodkin","raw_affiliation_strings":["1 Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and","institution_ids":["https://openalex.org/I124055696"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5004614832"],"corresponding_institution_ids":["https://openalex.org/I124055696"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.7736,"has_fulltext":true,"cited_by_count":47,"citation_normalized_percentile":{"value":0.8517998,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"32","issue":"8","first_page":"1238","last_page":"1240"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9070000052452087,"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":0.9070000052452087,"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":0.0568000003695488,"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":0.00930000003427267,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.7236008048057556},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7217464447021484},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4706548750400543},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4149305820465088},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.40235841274261475},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.36973726749420166},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35243725776672363},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1932704746723175},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14612838625907898},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08799979090690613}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7236008048057556},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7217464447021484},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4706548750400543},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4149305820465088},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.40235841274261475},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.36973726749420166},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35243725776672363},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1932704746723175},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14612838625907898},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08799979090690613},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btv748","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv748","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1238/49018410/bioinformatics_32_8_1238.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":"pmid:26704597","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26704597","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4824132","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4824132","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/8/1238","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/8/1238","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/e1994d7b-a628-4699-90ad-50c76a165233","is_oa":false,"landing_page_url":"https://curis.ku.dk/portal/da/publications/foldalign-25(e1994d7b-a628-4699-90ad-50c76a165233).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:pure.atira.dk:publications/e1994d7b-a628-4699-90ad-50c76a165233","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/e1994d7b-a628-4699-90ad-50c76a165233","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"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":"Sundfeld , D , Havgaard , J H , de Melo , A C M A & Gorodkin , J 2016 , ' Foldalign 2.5 : multithreaded implementation for pairwise structural RNA alignment ' , Bioinformatics , vol. 32 , no. 8 , pp. 1238-1240 . https://doi.org/10.1093/bioinformatics/btv748","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv748","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv748","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/8/1238/49018410/bioinformatics_32_8_1238.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/G1164920944","display_name":null,"funder_award_id":"99999","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"}],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320321999","display_name":"Lundbeckfonden","ror":"https://ror.org/03hz8wd80"},{"id":"https://openalex.org/F4320322975","display_name":"Danish e-Infrastructure Cooperation","ror":"https://ror.org/03ge1nb22"},{"id":"https://openalex.org/F4320327918","display_name":"H. Lundbeck A/S","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2268094462.pdf","grobid_xml":"https://content.openalex.org/works/W2268094462.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1522740115","https://openalex.org/W2018015544","https://openalex.org/W2095145214","https://openalex.org/W2114094654","https://openalex.org/W2122679732","https://openalex.org/W2132046933","https://openalex.org/W2137640371","https://openalex.org/W2140812101","https://openalex.org/W2147394603"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2942366970","https://openalex.org/W2807634898","https://openalex.org/W1692008701","https://openalex.org/W2597588799","https://openalex.org/W4360593462","https://openalex.org/W2562400057"],"abstract_inverted_index":{"MOTIVATION:":[0],"Structured":[1],"RNAs":[2,43,99],"can":[3,37],"be":[4],"hard":[5],"to":[6,116],"search":[7],"for":[8,32,52,96],"as":[9],"they":[10],"often":[11],"are":[12,21,131,141],"not":[13],"well":[14],"conserved":[15],"in":[16,23,35,108],"their":[17,24],"primary":[18],"structure":[19],"and":[20,56,100,127],"local":[22,39,84],"genomic":[25],"or":[26],"transcriptomic":[27],"context.":[28],"Thus,":[29],"the":[30,50,93,102,109,128],"need":[31],"tools":[33],"which":[34],"particular":[36],"make":[38],"structural":[40,85],"alignments":[41,86],"of":[42,69,87,119],"is":[44],"only":[45],"increasing.":[46],"RESULTS:":[47],"To":[48],"meet":[49],"demand":[51],"both":[53],"large-scale":[54],"screens":[55],"hands":[57],"on":[58],"analysis":[59],"through":[60],"web":[61,129],"servers,":[62],"we":[63],"present":[64],"a":[65,117],"new":[66],"multithreaded":[67],"version":[68],"Foldalign.":[70],"We":[71],"substantially":[72],"improve":[73,113],"execution":[74,114],"time":[75],"while":[76],"maintaining":[77],"all":[78],"previous":[79],"functionalities,":[80],"including":[81],"carrying":[82],"out":[83],"sequences":[88],"with":[89],"low":[90],"similarity.":[91],"Furthermore,":[92],"improvements":[94],"allow":[95],"comparing":[97],"longer":[98],"increasing":[101],"sequence":[103],"length.":[104],"For":[105],"example,":[106],"lengths":[107],"range":[110],"2000-6000":[111],"nucleotides":[112],"up":[115],"factor":[118],"five.":[120],"AVAILABILITY":[121],"AND":[122],"IMPLEMENTATION:":[123],"The":[124],"Foldalign":[125],"software":[126],"server":[130],"available":[132,142],"at":[133,143],"http://rth.dk/resources/foldalign":[134],"CONTACT:":[135],"gorodkin@rth.dk":[136],"SUPPLEMENTARY":[137],"INFORMATION:":[138],"Supplementary":[139],"data":[140],"Bioinformatics":[144],"online.":[145]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":3}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
