{"id":"https://openalex.org/W2804198854","doi":"https://doi.org/10.1093/bioinformatics/bty670","title":"copMEM: finding maximal exact matches via sampling both genomes","display_name":"copMEM: finding maximal exact matches via sampling both genomes","publication_year":2018,"publication_date":"2018-07-27","ids":{"openalex":"https://openalex.org/W2804198854","doi":"https://doi.org/10.1093/bioinformatics/bty670","mag":"2804198854","pmid":"https://pubmed.ncbi.nlm.nih.gov/30060142"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty670","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty670","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/4/677/27838459/bty670.pdf","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":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/4/677/27838459/bty670.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000229752","display_name":"Szymon Grabowski","orcid":"https://orcid.org/0000-0003-1714-1224"},"institutions":[{"id":"https://openalex.org/I188884621","display_name":"Lodz University of Technology","ror":"https://ror.org/00s8fpf52","country_code":"PL","type":"education","lineage":["https://openalex.org/I188884621"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Szymon Grabowski","raw_affiliation_strings":["Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90-924 d, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90-924 d, Poland","institution_ids":["https://openalex.org/I188884621"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051021897","display_name":"Wojciech Bieniecki","orcid":"https://orcid.org/0000-0003-1708-5760"},"institutions":[{"id":"https://openalex.org/I188884621","display_name":"Lodz University of Technology","ror":"https://ror.org/00s8fpf52","country_code":"PL","type":"education","lineage":["https://openalex.org/I188884621"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Wojciech Bieniecki","raw_affiliation_strings":["Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90-924 d, Poland"],"raw_orcid":"https://orcid.org/0000-0003-1708-5760","affiliations":[{"raw_affiliation_string":"Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90-924 d, Poland","institution_ids":["https://openalex.org/I188884621"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5051021897"],"corresponding_institution_ids":["https://openalex.org/I188884621"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.04366362,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"35","issue":"4","first_page":"677","last_page":"678"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.8583999872207642,"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"}},"topics":[{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.8583999872207642,"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"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.08309999853372574,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.03709999844431877,"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/genome","display_name":"Genome","score":0.7734503746032715},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.5925671458244324},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5061895251274109},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.49845027923583984},{"id":"https://openalex.org/keywords/coprime-integers","display_name":"Coprime integers","score":0.49738815426826477},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4588286578655243},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3320690393447876},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.329571008682251},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20157688856124878},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.17430412769317627},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10648050904273987},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.0547541081905365}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7734503746032715},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.5925671458244324},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5061895251274109},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.49845027923583984},{"id":"https://openalex.org/C23230895","wikidata":"https://www.wikidata.org/wiki/Q104752","display_name":"Coprime integers","level":2,"score":0.49738815426826477},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4588286578655243},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3320690393447876},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.329571008682251},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20157688856124878},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.17430412769317627},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10648050904273987},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0547541081905365},{"id":"https://openalex.org/C94915269","wikidata":"https://www.wikidata.org/wiki/Q1834857","display_name":"Detector","level":2,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bty670","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty670","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/4/677/27838459/bty670.pdf","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:30060142","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30060142","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":"Journal Article"},{"id":"pmh:oai:arXiv.org:1805.08816","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1805.08816","pdf_url":"https://arxiv.org/pdf/1805.08816","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},{"id":"mag:2804198854","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1805.08816.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1805.08816","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1805.08816","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty670","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty670","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/4/677/27838459/bty670.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2472939229","display_name":null,"funder_award_id":"501/12-24-1-5418","funder_id":"https://openalex.org/F4320326090","funder_display_name":"Politechnika L\u00f3dzka"}],"funders":[{"id":"https://openalex.org/F4320326090","display_name":"Politechnika L\u00f3dzka","ror":"https://ror.org/00s8fpf52"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2804198854.pdf","grobid_xml":"https://content.openalex.org/works/W2804198854.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2107282968","https://openalex.org/W2130062792","https://openalex.org/W2134283755","https://openalex.org/W2143531254","https://openalex.org/W2144560237","https://openalex.org/W2792368734"],"related_works":["https://openalex.org/W2778568625","https://openalex.org/W1995603520","https://openalex.org/W2951696997","https://openalex.org/W2965995818","https://openalex.org/W1767233502","https://openalex.org/W2336403425","https://openalex.org/W2161938817","https://openalex.org/W1572970249","https://openalex.org/W2058759221","https://openalex.org/W1998048394","https://openalex.org/W2792368734","https://openalex.org/W3120798773","https://openalex.org/W3160009835","https://openalex.org/W2104671007","https://openalex.org/W1970825859","https://openalex.org/W2008903345","https://openalex.org/W3005029022","https://openalex.org/W2099785809","https://openalex.org/W1513696542","https://openalex.org/W1588065748"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genome-to-genome":[1],"comparisons":[2],"require":[3],"designating":[4],"anchor":[5],"points,":[6],"which":[7],"are":[8,98],"given":[9],"by":[10],"Maximum":[11],"Exact":[12],"Matches":[13],"(MEMs)":[14],"between":[15,73],"their":[16],"sequences.":[17],"For":[18],"large":[19],"genomes":[20,78],"this":[21],"is":[22,36],"a":[23,43,62],"challenging":[24],"problem":[25],"and":[26,76],"the":[27,74],"performance":[28],"of":[29,69,87],"existing":[30],"solutions,":[31],"even":[32],"in":[33,79],"parallel":[34],"regimes,":[35],"not":[37],"quite":[38],"satisfactory.":[39],"RESULTS:":[40],"We":[41],"present":[42],"new":[44],"algorithm,":[45],"copMEM,":[46],"that":[47],"allows":[48],"to":[49],"sparsely":[50],"sample":[51],"both":[52],"input":[53],"genomes,":[54],"with":[55],"sampling":[56],"steps":[57],"being":[58,61],"coprime.":[59],"Despite":[60],"single-threaded":[63],"implementation,":[64],"copMEM":[65],"computes":[66],"all":[67],"MEMs":[68],"minimum":[70],"length":[71],"100":[72],"human":[75],"mouse":[77],"less":[80],"than":[81],"2":[82],"minutes,":[83],"using":[84],"7":[85],"GB":[86],"RAM":[88],"memory.":[89],"AVAILABILITY":[90],"AND":[91],"IMPLEMENTATION:":[92],"https://github.com/wbieniec/copmem.":[93],"SUPPLEMENTARY":[94],"DATA:":[95],"Supplementary":[96],"data":[97],"available":[99],"at":[100],"Bioinformatics":[101],"online.":[102]},"counts_by_year":[],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}