{"id":"https://openalex.org/W3127569522","doi":"https://doi.org/10.1186/s12859-021-03983-2","title":"IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences","display_name":"IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences","publication_year":2021,"publication_date":"2021-02-06","ids":{"openalex":"https://openalex.org/W3127569522","doi":"https://doi.org/10.1186/s12859-021-03983-2","mag":"3127569522","pmid":"https://pubmed.ncbi.nlm.nih.gov/33549041"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-03983-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03983-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03983-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03983-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030440060","display_name":"Hayam Alamro","orcid":"https://orcid.org/0000-0003-3157-8086"},"institutions":[{"id":"https://openalex.org/I106778892","display_name":"Princess Nourah bint Abdulrahman University","ror":"https://ror.org/05b0cyh02","country_code":"SA","type":"education","lineage":["https://openalex.org/I106778892"]},{"id":"https://openalex.org/I183935753","display_name":"King's College London","ror":"https://ror.org/0220mzb33","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I183935753"]}],"countries":["GB","SA"],"is_corresponding":false,"raw_author_name":"Hayam Alamro","raw_affiliation_strings":["Department of Informatics, King's College London, 30 Aldwych, London, UK","Department of Information Systems, Princess Nourah bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia","Department of Informatics [King's College London] (United Kingdom)","Princess Nourah Bint Abdulrahman University (Riyadh - Saudi Arabia)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, King's College London, 30 Aldwych, London, UK","institution_ids":["https://openalex.org/I183935753"]},{"raw_affiliation_string":"Department of Information Systems, Princess Nourah bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I106778892"]},{"raw_affiliation_string":"Department of Informatics [King's College London] (United Kingdom)","institution_ids":["https://openalex.org/I183935753"]},{"raw_affiliation_string":"Princess Nourah Bint Abdulrahman University (Riyadh - Saudi Arabia)","institution_ids":["https://openalex.org/I106778892"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007779501","display_name":"Mai Alzamel","orcid":"https://orcid.org/0000-0002-0862-7452"},"institutions":[{"id":"https://openalex.org/I183935753","display_name":"King's College London","ror":"https://ror.org/0220mzb33","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I183935753"]},{"id":"https://openalex.org/I28022161","display_name":"King Saud University","ror":"https://ror.org/02f81g417","country_code":"SA","type":"education","lineage":["https://openalex.org/I28022161"]}],"countries":["GB","SA"],"is_corresponding":false,"raw_author_name":"Mai Alzamel","raw_affiliation_strings":["Computer Science Department, King Saud University, Riyadh, Kingdom of Saudi Arabia","Department of Informatics, King's College London, 30 Aldwych, London, UK","KSU - King Saud University [Riyadh] (King Saud University, Riyadh 12372 - Saudi Arabia)","Department of Informatics [King's College London] (United Kingdom)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, King Saud University, Riyadh, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I28022161"]},{"raw_affiliation_string":"Department of Informatics, King's College London, 30 Aldwych, London, UK","institution_ids":["https://openalex.org/I183935753"]},{"raw_affiliation_string":"KSU - King Saud University [Riyadh] (King Saud University, Riyadh 12372 - Saudi Arabia)","institution_ids":["https://openalex.org/I28022161"]},{"raw_affiliation_string":"Department of Informatics [King's College London] (United Kingdom)","institution_ids":["https://openalex.org/I183935753"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058155947","display_name":"Costas S. Iliopoulos","orcid":"https://orcid.org/0000-0003-3909-0077"},"institutions":[{"id":"https://openalex.org/I183935753","display_name":"King's College London","ror":"https://ror.org/0220mzb33","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I183935753"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Costas S. Iliopoulos","raw_affiliation_strings":["Department of Informatics, King's College London, 30 Aldwych, London, UK","Department of Informatics [King's College London] (United Kingdom)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, King's College London, 30 Aldwych, London, UK","institution_ids":["https://openalex.org/I183935753"]},{"raw_affiliation_string":"Department of Informatics [King's College London] (United Kingdom)","institution_ids":["https://openalex.org/I183935753"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051275317","display_name":"Solon P. Pissis","orcid":"https://orcid.org/0000-0002-1445-1932"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832","https://openalex.org/I4405262988"]},{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["FR","NL"],"is_corresponding":false,"raw_author_name":"Solon P. Pissis","raw_affiliation_strings":["Centrum Wiskunde & Informatica, Amsterdam, The Netherlands. solon.pissis@cwi.nl","Vrije Universiteit Amsterdam, Amsterdam, The Netherlands. solon.pissis@cwi.nl","CWI - Centrum Wiskunde & Informatica (Science Park 123, 1098 XG Amsterdam - Netherlands)","VU - Vrije Universiteit Amsterdam [Amsterdam] (De Boelelaan 1105 1081 HV Amsterdam - Netherlands)","ERABLE - Equipe de recherche europ\u00e9enne en algorithmique et biologie formelle et exp\u00e9rimentale (Universit\u00e9 Claude Bernard (Lyon 1), \r\nCampus DOUA\r\n43, Boulevard du 11 Novembre 1918\r\n69622 Villeurbanne cedex - France)"],"raw_orcid":"https://orcid.org/0000-0002-1445-1932","affiliations":[{"raw_affiliation_string":"Centrum Wiskunde & Informatica, Amsterdam, The Netherlands. solon.pissis@cwi.nl","institution_ids":["https://openalex.org/I1341640284"]},{"raw_affiliation_string":"Vrije Universiteit Amsterdam, Amsterdam, The Netherlands. solon.pissis@cwi.nl","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"CWI - Centrum Wiskunde & Informatica (Science Park 123, 1098 XG Amsterdam - Netherlands)","institution_ids":["https://openalex.org/I1341640284"]},{"raw_affiliation_string":"VU - Vrije Universiteit Amsterdam [Amsterdam] (De Boelelaan 1105 1081 HV Amsterdam - Netherlands)","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"ERABLE - Equipe de recherche europ\u00e9enne en algorithmique et biologie formelle et exp\u00e9rimentale (Universit\u00e9 Claude Bernard (Lyon 1), \r\nCampus DOUA\r\n43, Boulevard du 11 Novembre 1918\r\n69622 Villeurbanne cedex - France)","institution_ids":["https://openalex.org/I100532134"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001989403","display_name":"Steven Watts","orcid":"https://orcid.org/0000-0002-1644-041X"},"institutions":[{"id":"https://openalex.org/I183935753","display_name":"King's College London","ror":"https://ror.org/0220mzb33","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I183935753"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Steven Watts","raw_affiliation_strings":["Department of Informatics, King's College London, 30 Aldwych, London, UK","Department of Informatics [King's College London] (United Kingdom)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, King's College London, 30 Aldwych, London, UK","institution_ids":["https://openalex.org/I183935753"]},{"raw_affiliation_string":"Department of Informatics [King's College London] (United Kingdom)","institution_ids":["https://openalex.org/I183935753"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.2213,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.78185083,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"51","last_page":"51"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5357999801635742,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5357999801635742,"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/T11269","display_name":"Algorithms and Data Compression","score":0.14579999446868896,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.06800000369548798,"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/computational-biology","display_name":"Computational biology","score":0.677960991859436},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5992652773857117},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5873878002166748},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5662127137184143},{"id":"https://openalex.org/keywords/inverted-repeat","display_name":"Inverted repeat","score":0.5475460290908813},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5179897546768188},{"id":"https://openalex.org/keywords/dna-profiling","display_name":"DNA profiling","score":0.5008659362792969},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.47452273964881897},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4664095640182495},{"id":"https://openalex.org/keywords/chemical-nomenclature","display_name":"Chemical nomenclature","score":0.42622295022010803},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20694932341575623},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12906011939048767},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.12265592813491821}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.677960991859436},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5992652773857117},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5873878002166748},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5662127137184143},{"id":"https://openalex.org/C51603236","wikidata":"https://www.wikidata.org/wiki/Q4852694","display_name":"Inverted repeat","level":4,"score":0.5475460290908813},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5179897546768188},{"id":"https://openalex.org/C79386861","wikidata":"https://www.wikidata.org/wiki/Q476697","display_name":"DNA profiling","level":3,"score":0.5008659362792969},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.47452273964881897},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4664095640182495},{"id":"https://openalex.org/C125832229","wikidata":"https://www.wikidata.org/wiki/Q6503924","display_name":"Chemical nomenclature","level":2,"score":0.42622295022010803},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20694932341575623},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12906011939048767},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.12265592813491821},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055029","descriptor_name":"Inverted Repeat Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055029","descriptor_name":"Inverted Repeat Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055029","descriptor_name":"Inverted Repeat Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055029","descriptor_name":"Inverted Repeat Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":10,"locations":[{"id":"doi:10.1186/s12859-021-03983-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03983-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03983-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33549041","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33549041","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:research.vu.nl:openaire/6de9afcd-18ba-43fd-8d7d-456e9cce120e","is_oa":true,"landing_page_url":"https://research.vu.nl/en/publications/6de9afcd-18ba-43fd-8d7d-456e9cce120e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401107","display_name":"VU Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Alamro, H, Alzamel, M, Iliopoulos, C S, Pissis, S P & Watts, S 2021, 'IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences', BMC Bioinformatics, vol. 22, 51, pp. 1-12. https://doi.org/10.1186/s12859-021-03983-2","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:cwi.nl:30612","is_oa":true,"landing_page_url":"https://ir.cwi.nl/pub/30612","pdf_url":"https://ir.cwi.nl/pub/30612/30612.pdf","source":{"id":"https://openalex.org/S7407055335","display_name":"Centrum Wiskunde & Informatica (CWI), the national research institute for mathematics and computer science in the Netherlands","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":"BMC Bioinformatics vol. 22","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:kclpure.kcl.ac.uk:publications/54c4249b-d626-41cd-a9ed-17c702661db3","is_oa":true,"landing_page_url":"https://kclpure.kcl.ac.uk/portal/en/publications/54c4249b-d626-41cd-a9ed-17c702661db3","pdf_url":"https://kclpure.kcl.ac.uk/ws/files/153944440/IUPACpal_efcient_identifcation_ALAMRO_Acc27Jan2021Epub6Feb_GOLD_VoR_CC_BY_.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Alamro , H , Alzamel , M , Iliopoulos , C S , Pissis , S P & Watts , S 2021 , ' IUPACpal : efficient identification of inverted repeats in IUPAC-encoded DNA sequences ' , BMC Bioinformatics , vol. 22 , no. 1 , 51 . https://doi.org/10.1186/s12859-021-03983-2","raw_type":"article"},{"id":"pmh:oai:HAL:hal-03498463v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03498463","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"BMC Bioinformatics, 2021, 22, pp.1-12. ⟨10.1186/s12859-021-03983-2⟩","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:5823246cbfe44575a0826d2ae10c4aff","is_oa":true,"landing_page_url":"https://doaj.org/article/5823246cbfe44575a0826d2ae10c4aff","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-12 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:6774410","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC7866733","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7866733","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7866733","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:research.vu.nl:publications/6de9afcd-18ba-43fd-8d7d-456e9cce120e","is_oa":true,"landing_page_url":"https://hdl.handle.net/1871.1/6de9afcd-18ba-43fd-8d7d-456e9cce120e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401107","display_name":"VU Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"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":"Alamro , H , Alzamel , M , Iliopoulos , C S , Pissis , S P & Watts , S 2021 , ' IUPACpal : efficient identification of inverted repeats in IUPAC-encoded DNA sequences ' , BMC Bioinformatics , vol. 22 , no. 1 , 51 , pp. 1-12 . https://doi.org/10.1186/s12859-021-03983-2","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-03983-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03983-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03983-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.5400000214576721,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G6697205189","display_name":null,"funder_award_id":"872539","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7373791487","display_name":null,"funder_award_id":"EP/M50788X-1.","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3127569522.pdf","grobid_xml":"https://content.openalex.org/works/W3127569522.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W386436423","https://openalex.org/W1504417041","https://openalex.org/W1651107957","https://openalex.org/W1977613481","https://openalex.org/W1981758687","https://openalex.org/W1990316578","https://openalex.org/W1996423252","https://openalex.org/W2021998028","https://openalex.org/W2036666081","https://openalex.org/W2056446691","https://openalex.org/W2072591969","https://openalex.org/W2078075583","https://openalex.org/W2082092341","https://openalex.org/W2089206902","https://openalex.org/W2091948567","https://openalex.org/W2104549677","https://openalex.org/W2112814753","https://openalex.org/W2117575253","https://openalex.org/W2118245974","https://openalex.org/W2128910215","https://openalex.org/W2158874082","https://openalex.org/W2165799971","https://openalex.org/W2547528004","https://openalex.org/W2809441573","https://openalex.org/W2952366981","https://openalex.org/W2978401557","https://openalex.org/W2984340848","https://openalex.org/W2986963718","https://openalex.org/W3006857885","https://openalex.org/W3013302872","https://openalex.org/W3039566339","https://openalex.org/W4212954813","https://openalex.org/W4254652536","https://openalex.org/W6979145273"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2765674682","https://openalex.org/W2095596879","https://openalex.org/W4251955477","https://openalex.org/W4386027229","https://openalex.org/W2065541177","https://openalex.org/W2171646645","https://openalex.org/W2473178225","https://openalex.org/W4212769910","https://openalex.org/W4235765434"],"abstract_inverted_index":{"BACKGROUND:":[0],"An":[1],"inverted":[2,81,96,128],"repeat":[3],"is":[4,137],"a":[5,16,44,114],"DNA":[6,85],"sequence":[7,53],"followed":[8],"downstream":[9],"by":[10],"its":[11],"reverse":[12],"complement,":[13],"potentially":[14],"with":[15,36,118,132,140],"gap":[17],"in":[18,25,83,94],"the":[19,62,95,100],"centre.":[20],"Inverted":[21],"repeats":[22,82,129],"are":[23],"found":[24],"both":[26],"prokaryotic":[27],"and":[28,31,92,134],"eukaryotic":[29],"genomes":[30],"they":[32],"have":[33],"been":[34],"linked":[35],"countless":[37],"possible":[38],"functions.":[39],"Many":[40],"international":[41],"consortia":[42],"provide":[43],"comprehensive":[45],"description":[46],"of":[47,65,80,142],"common":[48],"genetic":[49],"variation":[50,68],"making":[51],"alternative":[52],"representations,":[54],"such":[55,66],"as":[56],"IUPAC":[57],"encoding,":[58],"necessary":[59],"for":[60,77,89],"leveraging":[61],"full":[63],"potential":[64,90],"broad":[67],"datasets.":[69],"RESULTS:":[70],"We":[71,120],"present":[72],"IUPACPAL,":[73],"an":[74],"exact":[75],"tool":[76],"efficient":[78],"identification":[79],"IUPAC-encoded":[84],"sequences":[86],"allowing":[87],"also":[88,138],"mismatches":[91],"gaps":[93],"repeats.":[97],"CONCLUSION:":[98],"Within":[99],"parameters":[101],"that":[102,109,122,135],"were":[103],"tested,":[104],"our":[105],"experimental":[106],"results":[107],"show":[108,121],"IUPACPAL":[110,123],"compares":[111],"favourably":[112],"to":[113],"similar":[115],"application":[116],"packaged":[117],"EMBOSS.":[119],"identifies":[124],"many":[125],"previously":[126],"unidentified":[127],"when":[130],"compared":[131],"EMBOSS,":[133],"this":[136],"performed":[139],"orders":[141],"magnitude":[143],"improved":[144],"speed.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":8}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}