{"id":"https://openalex.org/W2996083167","doi":"https://doi.org/10.1093/bioinformatics/btz928","title":"pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm","display_name":"pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm","publication_year":2019,"publication_date":"2019-12-09","ids":{"openalex":"https://openalex.org/W2996083167","doi":"https://doi.org/10.1093/bioinformatics/btz928","mag":"2996083167","pmid":"https://pubmed.ncbi.nlm.nih.gov/31830256"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz928","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz928","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081886374","display_name":"Dominika Labudov\u00e1","orcid":null},"institutions":[{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Dominika Labudov\u00e1","raw_affiliation_strings":["IT4Innovations Centre of Excellence, Faculty of Information Technology , Brno University of Technology, Brno 61266, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IT4Innovations Centre of Excellence, Faculty of Information Technology , Brno University of Technology, Brno 61266, Czech Republic","institution_ids":["https://openalex.org/I60587646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036193890","display_name":"Ji\u0159\u00ed Hon","orcid":"https://orcid.org/0000-0002-3321-9629"},"institutions":[{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ji\u0159\u00ed Hon","raw_affiliation_strings":["IT4Innovations Centre of Excellence, Faculty of Information Technology , Brno University of Technology, Brno 61266, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IT4Innovations Centre of Excellence, Faculty of Information Technology , Brno University of Technology, Brno 61266, Czech Republic","institution_ids":["https://openalex.org/I60587646"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082104022","display_name":"Matej Lexa","orcid":"https://orcid.org/0000-0002-4213-5259"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210089928","display_name":"Czech Academy of Sciences, Institute of Biophysics","ror":"https://ror.org/00angvn73","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210089928"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Matej Lexa","raw_affiliation_strings":["Department of Machine Learning and Data Processing, Faculty of Informatics, Masaryk University , Brno 60200, Czech Republic","Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , Brno 61200, Czech Republic"],"raw_orcid":"https://orcid.org/0000-0002-4213-5259","affiliations":[{"raw_affiliation_string":"Department of Machine Learning and Data Processing, Faculty of Informatics, Masaryk University , Brno 60200, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , Brno 61200, Czech Republic","institution_ids":["https://openalex.org/I4210089928"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082104022"],"corresponding_institution_ids":["https://openalex.org/I21449261","https://openalex.org/I4210089928"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9114,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.7449005,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"8","first_page":"2584","last_page":"2586"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9740999937057495,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9740999937057495,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.006200000178068876,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.003700000001117587,"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/computer-science","display_name":"Computer science","score":0.6710242033004761},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5529443025588989},{"id":"https://openalex.org/keywords/g-quadruplex","display_name":"G-quadruplex","score":0.5222747325897217},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10746195912361145},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.05856475234031677}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6710242033004761},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5529443025588989},{"id":"https://openalex.org/C83762044","wikidata":"https://www.wikidata.org/wiki/Q411641","display_name":"G-quadruplex","level":3,"score":0.5222747325897217},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10746195912361145},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.05856475234031677},{"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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz928","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz928","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31830256","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31830256","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}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6000000238418579,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2842154333","display_name":null,"funder_award_id":"FIT-S-17-3964","funder_id":"https://openalex.org/F4320322748","funder_display_name":"Vysok\u00e9 U\u010den\u00ed Technick\u00e9 v Brn\u011b"},{"id":"https://openalex.org/G8923270395","display_name":"The role of transposable elements in the dynamics of plant genomes","funder_award_id":"GA18-00258S","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"}],"funders":[{"id":"https://openalex.org/F4320321006","display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","ror":"https://ror.org/01pv73b02"},{"id":"https://openalex.org/F4320322748","display_name":"Vysok\u00e9 U\u010den\u00ed Technick\u00e9 v Brn\u011b","ror":"https://ror.org/03613d656"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1450574606","https://openalex.org/W2290989326","https://openalex.org/W2730926509","https://openalex.org/W2802586507","https://openalex.org/W2806209637","https://openalex.org/W2918361769","https://openalex.org/W2923522997","https://openalex.org/W2932086320","https://openalex.org/W2963145526","https://openalex.org/W2997085008","https://openalex.org/W6628411584","https://openalex.org/W6765747507"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2320293038","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W2766452385"],"abstract_inverted_index":{"MOTIVATION:":[0],"G-quadruplex":[1],"is":[2,42],"a":[3,32,124,131],"DNA":[4],"or":[5],"RNA":[6],"form":[7],"in":[8,22,40,52,66],"which":[9],"four":[10],"guanine-rich":[11],"regions":[12],"are":[13,28,116,158],"held":[14],"together":[15],"by":[16],"base":[17],"pairing":[18],"between":[19],"guanine":[20],"nucleotides":[21],"coordination":[23],"with":[24],"potassium":[25],"ions.":[26],"G-quadruplexes":[27],"increasingly":[29],"seen":[30],"as":[31,70],"biologically":[33],"important":[34],"component":[35],"of":[36,102,123,127,135,144],"genomes.":[37],"Their":[38],"detection":[39],"vivo":[41],"problematic;":[43],"however,":[44],"sequencing":[45],"and":[46,68,83,109],"spectrometric":[47],"techniques":[48],"exist":[49],"for":[50,61,76,81,133],"their":[51],"vitro":[53],"detection.":[54],"We":[55,74,88,98],"previously":[56],"devised":[57],"the":[58,100,103,121],"pqsfinder":[59,80,94],"algorithm":[60,105],"PQS":[62,113],"identification,":[63],"implemented":[64],"it":[65],"C++":[67],"published":[69],"an":[71],"R/Bioconductor":[72],"package.":[73],"looked":[75],"ways":[77],"to":[78,106,146],"optimize":[79],"faster":[82],"user-friendly":[84],"sequence":[85,136],"analysis.":[86],"RESULTS:":[87],"identified":[89],"two":[90],"weak":[91],"points":[92],"where":[93],"could":[95],"be":[96],"optimized.":[97],"modified":[99],"internals":[101],"recursive":[104],"avoid":[107],"matching":[108],"scoring":[110],"many":[111],"sub-optimal":[112],"conformations":[114],"that":[115,139],"later":[117],"discarded.":[118],"To":[119],"accommodate":[120],"needs":[122],"broader":[125],"range":[126],"users,":[128],"we":[129],"created":[130],"website":[132],"submission":[134],"analysis":[137],"jobs":[138],"does":[140],"not":[141],"require":[142],"knowledge":[143],"R":[145],"use":[147],"pqsfinder.":[148],"AVAILABILITY":[149],"AND":[150],"IMPLEMENTATION:":[151],"https://pqsfinder.fi.muni.cz,":[152],"https://bioconductor.org/packages/pqsfinder.":[153],"SUPPLEMENTARY":[154],"INFORMATION:":[155],"Supplementary":[156],"data":[157],"available":[159],"at":[160],"Bioinformatics":[161],"online.":[162]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
