{"id":"https://openalex.org/W2128910215","doi":"https://doi.org/10.1093/bioinformatics/btt651","title":"A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences","display_name":"A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences","publication_year":2013,"publication_date":"2013-11-08","ids":{"openalex":"https://openalex.org/W2128910215","doi":"https://doi.org/10.1093/bioinformatics/btt651","mag":"2128910215","pmid":"https://pubmed.ncbi.nlm.nih.gov/24215021"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt651","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt651","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/A5065688740","display_name":"Sutharzan Sreeskandarajan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097978","display_name":"Institute of Plant Protection","ror":"https://ror.org/0111f7045","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210097978","https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]},{"id":"https://openalex.org/I4210138501","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Sutharzan Sreeskandarajan","raw_affiliation_strings":["1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China","institution_ids":["https://openalex.org/I4210138501","https://openalex.org/I4210097978"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036377369","display_name":"Michelle M. Flowers","orcid":null},"institutions":[{"id":"https://openalex.org/I4210138501","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]},{"id":"https://openalex.org/I4210097978","display_name":"Institute of Plant Protection","ror":"https://ror.org/0111f7045","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210097978","https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Michelle M. Flowers","raw_affiliation_strings":["1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China","institution_ids":["https://openalex.org/I4210138501","https://openalex.org/I4210097978"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027197880","display_name":"John Karro","orcid":null},"institutions":[{"id":"https://openalex.org/I4210097978","display_name":"Institute of Plant Protection","ror":"https://ror.org/0111f7045","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210097978","https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]},{"id":"https://openalex.org/I4210138501","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"John E. Karro","raw_affiliation_strings":["1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China","institution_ids":["https://openalex.org/I4210138501","https://openalex.org/I4210097978"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101531536","display_name":"Chun Liang","orcid":"https://orcid.org/0000-0003-1996-6027"},"institutions":[{"id":"https://openalex.org/I4210138501","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]},{"id":"https://openalex.org/I4210097978","display_name":"Institute of Plant Protection","ror":"https://ror.org/0111f7045","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210097978","https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chun Liang","raw_affiliation_strings":["1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biology, 2Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and 3State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China","institution_ids":["https://openalex.org/I4210138501","https://openalex.org/I4210097978"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5065688740"],"corresponding_institution_ids":["https://openalex.org/I4210097978","https://openalex.org/I4210138501"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1966,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.78956234,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"30","issue":"6","first_page":"887","last_page":"888"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.7562999725341797,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.7562999725341797,"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":0.040800001472234726,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.02850000001490116,"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/palindrome","display_name":"Palindrome","score":0.6974666118621826},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6595593094825745},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.6150440573692322},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4742559492588043},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47293949127197266},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.43366241455078125},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4302939176559448},{"id":"https://openalex.org/keywords/prime","display_name":"Prime (order theory)","score":0.4243670403957367},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3549705147743225},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3247339725494385},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29849934577941895},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14935222268104553},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12087032198905945},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.08214935660362244}],"concepts":[{"id":"https://openalex.org/C44667518","wikidata":"https://www.wikidata.org/wiki/Q12321","display_name":"Palindrome","level":4,"score":0.6974666118621826},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6595593094825745},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.6150440573692322},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4742559492588043},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47293949127197266},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.43366241455078125},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4302939176559448},{"id":"https://openalex.org/C184992742","wikidata":"https://www.wikidata.org/wiki/Q7243229","display_name":"Prime (order theory)","level":2,"score":0.4243670403957367},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3549705147743225},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3247339725494385},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29849934577941895},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14935222268104553},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12087032198905945},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.08214935660362244},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","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":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","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":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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt651","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt651","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:24215021","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24215021","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:europepmc.org:3323457","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3957078","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G775009472","display_name":null,"funder_award_id":"1R15GM94732-1 A1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8642163011","display_name":null,"funder_award_id":"O953215","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W655500139","https://openalex.org/W1569990927","https://openalex.org/W1967297336","https://openalex.org/W1990139926","https://openalex.org/W1992735147","https://openalex.org/W1996423252","https://openalex.org/W2001246832","https://openalex.org/W2005454205","https://openalex.org/W2013467774","https://openalex.org/W2036666081","https://openalex.org/W2038795301","https://openalex.org/W2059650806","https://openalex.org/W2089206902","https://openalex.org/W2153562063","https://openalex.org/W2157560852","https://openalex.org/W2171331964"],"related_works":["https://openalex.org/W2136569355","https://openalex.org/W4214506306","https://openalex.org/W2940487742","https://openalex.org/W4323366524","https://openalex.org/W1980577621","https://openalex.org/W2477304139","https://openalex.org/W1986616196","https://openalex.org/W2619402950","https://openalex.org/W1677680917","https://openalex.org/W2580705150"],"abstract_inverted_index":{"SUMMARY:":[0],"Palindromic":[1],"sequences,":[2],"or":[3,116],"inverted":[4],"repeats":[5],"(IRs),":[6],"in":[7,42,97],"DNA":[8,18,21],"sequences":[9],"involve":[10],"important":[11],"biological":[12],"processes":[13],"such":[14],"as":[15,77],"DNA-protein":[16],"binding,":[17],"replication":[19],"and":[20,45,100],"transposition.":[22],"Development":[23],"of":[24,30,39,69],"bioinformatics":[25],"tools":[26],"that":[27,57],"are":[28,122],"capable":[29],"accurately":[31],"detecting":[32,98],"perfect":[33,82],"IRs":[34],"can":[35],"enable":[36],"genome-wide":[37],"studies":[38],"IR":[40,83],"patterns":[41],"both":[43],"prokaryotes":[44],"eukaryotes.":[46],"Different":[47],"from":[48],"conventional":[49],"string-comparison":[50],"approaches,":[51],"we":[52],"propose":[53],"a":[54,59,65,78,94],"novel":[55],"algorithm":[56,76],"uses":[58],"cumulative":[60],"score":[61],"system":[62],"based":[63],"on":[64,112],"prime":[66],"number":[67],"representation":[68],"nucleotide":[70],"bases.":[71],"We":[72],"then":[73],"implemented":[74],"this":[75],"MATLAB-based":[79],"program":[80,92],"for":[81],"detection.":[84],"In":[85],"comparison":[86],"with":[87],"other":[88],"existing":[89],"tools,":[90],"our":[91],"demonstrates":[93],"high":[95],"accuracy":[96],"nested":[99],"overlapping":[101],"IRs.":[102],"AVAILABILITY":[103],"AND":[104],"IMPLEMENTATION:":[105],"The":[106],"source":[107],"code":[108],"is":[109],"freely":[110],"available":[111,123],"(http://bioinfolab.miamioh.edu/bioinfolab/palindrome.php)":[113],"CONTACT:":[114],"liangc@miamioh.edu":[115],"karroje@miamioh.edu":[117],"SUPPLEMENTARY":[118],"INFORMATION:":[119],"Supplementary":[120],"data":[121],"at":[124],"Bioinformatics":[125],"online.":[126]},"counts_by_year":[{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
