{"id":"https://openalex.org/W2766455560","doi":"https://doi.org/10.1142/s0219720017400091","title":"Efficient RNA structure comparison algorithms","display_name":"Efficient RNA structure comparison algorithms","publication_year":2017,"publication_date":"2017-10-19","ids":{"openalex":"https://openalex.org/W2766455560","doi":"https://doi.org/10.1142/s0219720017400091","mag":"2766455560"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720017400091","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720017400091","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"],"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/A5072963545","display_name":"Abdullah N. Arslan","orcid":"https://orcid.org/0000-0002-3979-6371"},"institutions":[{"id":"https://openalex.org/I206651237","display_name":"East Texas A&M University","ror":"https://ror.org/01red3556","country_code":"US","type":"education","lineage":["https://openalex.org/I206651237"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Abdullah N. Arslan","raw_affiliation_strings":["Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA","institution_ids":["https://openalex.org/I206651237"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086472443","display_name":"Jithendar Anandan","orcid":null},"institutions":[{"id":"https://openalex.org/I206651237","display_name":"East Texas A&M University","ror":"https://ror.org/01red3556","country_code":"US","type":"education","lineage":["https://openalex.org/I206651237"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jithendar Anandan","raw_affiliation_strings":["Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA","institution_ids":["https://openalex.org/I206651237"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003017636","display_name":"Eric Fry","orcid":null},"institutions":[{"id":"https://openalex.org/I206651237","display_name":"East Texas A&M University","ror":"https://ror.org/01red3556","country_code":"US","type":"education","lineage":["https://openalex.org/I206651237"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Fry","raw_affiliation_strings":["Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA","institution_ids":["https://openalex.org/I206651237"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031523836","display_name":"Keith Monschke","orcid":null},"institutions":[{"id":"https://openalex.org/I206651237","display_name":"East Texas A&M University","ror":"https://ror.org/01red3556","country_code":"US","type":"education","lineage":["https://openalex.org/I206651237"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keith Monschke","raw_affiliation_strings":["Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA","institution_ids":["https://openalex.org/I206651237"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000520482","display_name":"Nitin Ganneboina","orcid":null},"institutions":[{"id":"https://openalex.org/I206651237","display_name":"East Texas A&M University","ror":"https://ror.org/01red3556","country_code":"US","type":"education","lineage":["https://openalex.org/I206651237"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nitin Ganneboina","raw_affiliation_strings":["Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA","institution_ids":["https://openalex.org/I206651237"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073127461","display_name":"Jason Bowerman","orcid":null},"institutions":[{"id":"https://openalex.org/I206651237","display_name":"East Texas A&M University","ror":"https://ror.org/01red3556","country_code":"US","type":"education","lineage":["https://openalex.org/I206651237"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason Bowerman","raw_affiliation_strings":["Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A&amp;M University-Commerce, Commerce, TX 75428, USA","institution_ids":["https://openalex.org/I206651237"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5072963545"],"corresponding_institution_ids":["https://openalex.org/I206651237"],"apc_list":null,"apc_paid":null,"fwci":0.5606,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.67193851,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"15","issue":"06","first_page":"1740009","last_page":"1740009"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9958999752998352,"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":0.9954000115394592,"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/suffix-array","display_name":"Suffix array","score":0.7450291514396667},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.7154887914657593},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.610785186290741},{"id":"https://openalex.org/keywords/substructure","display_name":"Substructure","score":0.5668365955352783},{"id":"https://openalex.org/keywords/compressed-suffix-array","display_name":"Compressed suffix array","score":0.5649746060371399},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5588652491569519},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5515890717506409},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5272516012191772},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.4991109371185303},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.45974403619766235},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.4236131012439728},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41450417041778564},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3953211307525635},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3252714276313782},{"id":"https://openalex.org/keywords/suffix-tree","display_name":"Suffix tree","score":0.29365307092666626}],"concepts":[{"id":"https://openalex.org/C2779259728","wikidata":"https://www.wikidata.org/wiki/Q281472","display_name":"Suffix array","level":3,"score":0.7450291514396667},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.7154887914657593},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.610785186290741},{"id":"https://openalex.org/C99679407","wikidata":"https://www.wikidata.org/wiki/Q56761637","display_name":"Substructure","level":2,"score":0.5668365955352783},{"id":"https://openalex.org/C100903775","wikidata":"https://www.wikidata.org/wiki/Q5157028","display_name":"Compressed suffix array","level":4,"score":0.5649746060371399},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5588652491569519},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5515890717506409},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5272516012191772},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.4991109371185303},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.45974403619766235},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.4236131012439728},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41450417041778564},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3953211307525635},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3252714276313782},{"id":"https://openalex.org/C2781166958","wikidata":"https://www.wikidata.org/wiki/Q1426863","display_name":"Suffix tree","level":3,"score":0.29365307092666626},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1142/s0219720017400091","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720017400091","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"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1543796220","https://openalex.org/W1568850903","https://openalex.org/W1635828033","https://openalex.org/W1834458707","https://openalex.org/W1994042976","https://openalex.org/W2023206235","https://openalex.org/W2030962049","https://openalex.org/W2040176884","https://openalex.org/W2055043387","https://openalex.org/W2077770566","https://openalex.org/W2096327663","https://openalex.org/W2119377644","https://openalex.org/W2127375279","https://openalex.org/W2142056356","https://openalex.org/W2143407915","https://openalex.org/W2158381555","https://openalex.org/W2162224067","https://openalex.org/W4232859119","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W2003608043","https://openalex.org/W3113848129","https://openalex.org/W1630495895","https://openalex.org/W2136043658","https://openalex.org/W2081157440","https://openalex.org/W2582547125","https://openalex.org/W2601653602","https://openalex.org/W1485068757","https://openalex.org/W2766455560","https://openalex.org/W2148315173"],"abstract_inverted_index":{"Recently":[0],"proposed":[1,34],"relative":[2],"addressing-based":[3],"([Formula:":[4],"see":[5,66],"text])":[6],"RNA":[7,17,62,71,89,156,176],"secondary":[8],"structure":[9,18,72,177,181],"representation":[10],"has":[11,32,93],"important":[12],"features":[13],"by":[14,164],"which":[15],"an":[16,103],"database":[19],"can":[20,159],"be":[21,160],"stored":[22],"into":[23],"a":[24,50,83,179],"suffix":[25,41],"array.":[26,42],"A":[27],"fast":[28,51],"substructure":[29,45,58],"search":[30,38,46,166],"algorithm":[31,52,104,115,120],"been":[33],"based":[35],"on":[36,39],"binary":[37],"this":[40,44,107,119],"Using":[43],"algorithm,":[47],"we":[48,101,135],"present":[49],"that":[53,105,116,158],"finds":[54],"the":[55,131,137,165,174],"largest":[56],"common":[57,125],"of":[59],"given":[60,180],"multiple":[61,70,88],"structures":[63],"in":[64,77,127],"[Formula:":[65],"text]":[67],"format.":[68],"The":[69],"comparison":[73,114],"problem":[74,85,92,108],"is":[75],"NP-hard":[76],"its":[78],"general":[79],"formulation.":[80],"We":[81,110],"introduced":[82],"new":[84,132],"for":[86,154,171],"comparing":[87],"structures.":[90],"This":[91,144],"more":[94],"strict":[95],"similarity":[96],"definition":[97],"and":[98,100,168],"objective,":[99],"propose":[102],"solves":[106],"efficiently.":[109],"also":[111,147],"develop":[112],"another":[113,169],"iteratively":[117],"calls":[118],"to":[121],"locate":[122],"nonoverlapping":[123],"large":[124],"substructures":[126,157],"compared":[128],"RNAs.":[129],"With":[130],"resulting":[133],"tools,":[134],"improved":[136],"RNASSAC":[138],"website":[139,145],"(linked":[140],"from":[141,178],"http://faculty.tamuc.edu/aarslan":[142],").":[143],"now":[146],"includes":[148],"two":[149],"drawing":[150,173],"tools:":[151],"one":[152,170],"specialized":[153],"preparing":[155],"used":[161],"as":[162],"input":[163],"tool,":[167],"automatically":[172],"entire":[175],"sequence.":[182]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2017-11-10T00:00:00"}
