{"id":"https://openalex.org/W4353096517","doi":"https://doi.org/10.1016/j.simpa.2023.100498","title":"Feature-overlapper: The tool for DNA analysis overlap","display_name":"Feature-overlapper: The tool for DNA analysis overlap","publication_year":2023,"publication_date":"2023-03-22","ids":{"openalex":"https://openalex.org/W4353096517","doi":"https://doi.org/10.1016/j.simpa.2023.100498"},"language":"en","primary_location":{"id":"doi:10.1016/j.simpa.2023.100498","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.simpa.2023.100498","pdf_url":null,"source":{"id":"https://openalex.org/S4210180398","display_name":"Software Impacts","issn_l":"2665-9638","issn":["2665-9638"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Software Impacts","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.simpa.2023.100498","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102904750","display_name":"Jan Havl\u00edk","orcid":"https://orcid.org/0000-0001-5600-2935"},"institutions":[{"id":"https://openalex.org/I56081889","display_name":"Mendel University in Brno","ror":"https://ror.org/058aeep47","country_code":"CZ","type":"education","lineage":["https://openalex.org/I56081889"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Jan Havl\u00edk","raw_affiliation_strings":["Department of Informatics, Faculty of Business and Economics, Mendel University in Brno, Zem\u011bd\u011blsk\u00e1 1, 613 00 Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Faculty of Business and Economics, Mendel University in Brno, Zem\u011bd\u011blsk\u00e1 1, 613 00 Brno, Czech Republic","institution_ids":["https://openalex.org/I56081889"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064129508","display_name":"V\u00e1clav Br\u00e1zda","orcid":"https://orcid.org/0000-0003-2837-4226"},"institutions":[{"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":false,"raw_author_name":"V\u00e1clav Br\u00e1zda","raw_affiliation_strings":["Institute of Biophysics of the Czech Academy of Sciences, Kr\u00e1lovopolsk\u00e1 135, 612 65 Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Biophysics of the Czech Academy of Sciences, Kr\u00e1lovopolsk\u00e1 135, 612 65 Brno, Czech Republic","institution_ids":["https://openalex.org/I4210089928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103075069","display_name":"Kamil Stan\u011bk","orcid":"https://orcid.org/0000-0002-8131-1948"},"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":"Kamil Stan\u011bk","raw_affiliation_strings":["Faculty of Mechanical Engineering, Brno University of Technology, Technick\u00e1 2896/2, 616 69 Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Faculty of Mechanical Engineering, Brno University of Technology, Technick\u00e1 2896/2, 616 69 Brno, Czech Republic","institution_ids":["https://openalex.org/I60587646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112411829","display_name":"Michal Je\u017eek","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":"Michal Je\u017eek","raw_affiliation_strings":["Faculty of Mechanical Engineering, Brno University of Technology, Technick\u00e1 2896/2, 616 69 Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Faculty of Mechanical Engineering, Brno University of Technology, Technick\u00e1 2896/2, 616 69 Brno, Czech Republic","institution_ids":["https://openalex.org/I60587646"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004352018","display_name":"Ji\u0159\u00ed \u0160\u0165astn\u00fd","orcid":"https://orcid.org/0000-0003-3724-6357"},"institutions":[{"id":"https://openalex.org/I56081889","display_name":"Mendel University in Brno","ror":"https://ror.org/058aeep47","country_code":"CZ","type":"education","lineage":["https://openalex.org/I56081889"]},{"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 \u0160t\u2019astn\u00fd","raw_affiliation_strings":["Faculty of Mechanical Engineering, Brno University of Technology, Technick\u00e1 2896/2, 616 69 Brno, Czech Republic","Department of Informatics, Faculty of Business and Economics, Mendel University in Brno, Zem\u011bd\u011blsk\u00e1 1, 613 00 Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Faculty of Mechanical Engineering, Brno University of Technology, Technick\u00e1 2896/2, 616 69 Brno, Czech Republic","institution_ids":["https://openalex.org/I60587646"]},{"raw_affiliation_string":"Department of Informatics, Faculty of Business and Economics, Mendel University in Brno, Zem\u011bd\u011blsk\u00e1 1, 613 00 Brno, Czech Republic","institution_ids":["https://openalex.org/I56081889"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5102904750"],"corresponding_institution_ids":["https://openalex.org/I56081889"],"apc_list":{"value":450,"currency":"USD","value_usd":450},"apc_paid":{"value":450,"currency":"USD","value_usd":450},"fwci":0.1543,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.56933937,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"16","issue":null,"first_page":"100498","last_page":"100498"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9660999774932861,"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":0.9660999774932861,"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":0.9355000257492065,"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/T10751","display_name":"Forensic and Genetic Research","score":0.9327999949455261,"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/feature","display_name":"Feature (linguistics)","score":0.5904369950294495},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4740143418312073},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42728912830352783},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3645137548446655},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33911317586898804},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28029805421829224},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.08340826630592346}],"concepts":[{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5904369950294495},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4740143418312073},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42728912830352783},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3645137548446655},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33911317586898804},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28029805421829224},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.08340826630592346},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1016/j.simpa.2023.100498","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.simpa.2023.100498","pdf_url":null,"source":{"id":"https://openalex.org/S4210180398","display_name":"Software Impacts","issn_l":"2665-9638","issn":["2665-9638"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Software Impacts","raw_type":"journal-article"},{"id":"pmh:oai:dspace.vutbr.cz:11012/213660","is_oa":true,"landing_page_url":"http://hdl.handle.net/11012/213660","pdf_url":"https://dspace.vut.cz/bitstreams/e30324cd-7969-4c10-bd3c-29f592f01c45/download","source":{"id":"https://openalex.org/S4306400317","display_name":"Brno University of Technology Digital Library (Brno University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I60587646","host_organization_name":"Brno University of Technology","host_organization_lineage":["https://openalex.org/I60587646"],"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":"Software Impacts. 2023, vol. 16, issue 5, p. 1-4.","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1016/j.simpa.2023.100498","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.simpa.2023.100498","pdf_url":null,"source":{"id":"https://openalex.org/S4210180398","display_name":"Software Impacts","issn_l":"2665-9638","issn":["2665-9638"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Software Impacts","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320325362","display_name":"Mendelova Univerzita v Brn\u011b","ror":"https://ror.org/058aeep47"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2073722866","https://openalex.org/W2164414740","https://openalex.org/W2410769199","https://openalex.org/W2513764101","https://openalex.org/W2913145970","https://openalex.org/W2950609079","https://openalex.org/W3163990482","https://openalex.org/W3201182739","https://openalex.org/W3210830956","https://openalex.org/W3217268895","https://openalex.org/W4312056535","https://openalex.org/W6764206669","https://openalex.org/W6795410112","https://openalex.org/W6847449775"],"related_works":["https://openalex.org/W2033914206","https://openalex.org/W2146076056","https://openalex.org/W2163831990","https://openalex.org/W3003836766","https://openalex.org/W2046077695","https://openalex.org/W2378160586","https://openalex.org/W2042327336","https://openalex.org/W2546942002","https://openalex.org/W2970216048","https://openalex.org/W2382607599"],"abstract_inverted_index":{"This":[0],"contribution":[1],"puts":[2],"focus":[3],"on":[4],"a":[5],"command":[6],"line":[7],"tool,":[8],"which":[9,35],"enables":[10],"detection":[11],"and":[12,20,27,63,82],"analysis":[13],"of":[14,93],"overlapping":[15],"regions":[16,45],"between":[17,47],"G-quadruplexes,":[18],"R-loops":[19,28,62],"genome":[21,68],"annotations":[22,69],"for":[23,41,78],"selected":[24],"genomes.":[25],"G-quadruplexes":[26],"are":[29],"structures":[30,49],"with":[31,53,70],"high":[32,71],"Guanine":[33],"density,":[34],"is":[36,83],"an":[37],"important":[38],"creation":[39],"factor":[40],"both":[42,48],"structures.":[43],"Common":[44],"(overlap)":[46],"can":[50],"provide":[51],"us":[52],"better":[54],"possibility":[55],"to":[56,60,90],"create":[57],"precise":[58],"model":[59],"detect":[61],"valuable":[64],"insights":[65],"when":[66],"inspecting":[67],"R-loop":[72],"density.":[73],"The":[74],"tool":[75],"was":[76],"used":[77],"multiple":[79],"research":[80],"projects":[81],"under":[84],"constant":[85],"development":[86],"bringing":[87],"new":[88],"features":[89],"the":[91],"world":[92],"bioinformatics.":[94]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
