{"id":"https://openalex.org/W2115039095","doi":"https://doi.org/10.1093/bioinformatics/btg466","title":"me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements","display_name":"me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements","publication_year":2004,"publication_date":"2004-01-22","ids":{"openalex":"https://openalex.org/W2115039095","doi":"https://doi.org/10.1093/bioinformatics/btg466","mag":"2115039095","pmid":"https://pubmed.ncbi.nlm.nih.gov/14990458"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg466","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg466","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/4/588/48905217/bioinformatics_20_4_588.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":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/20/4/588/48905217/bioinformatics_20_4_588.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5106697428","display_name":"Kevin Murphy","orcid":null},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kevin Murphy","raw_affiliation_strings":["Division of Oncology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia 19104-4318, USA","Division of Oncology, Children's Hospital of Philadelphia;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Oncology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia 19104-4318, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Division of Oncology, Children's Hospital of Philadelphia;","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101745098","display_name":"T.G. Teeni Janet Raj","orcid":"https://orcid.org/0000-0001-6410-4923"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Towfique Raj","raw_affiliation_strings":["Division of Oncology, Children's Hospital of Philadelphia;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Oncology, Children's Hospital of Philadelphia;","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110681915","display_name":"R. Scott Winters","orcid":"https://orcid.org/0000-0002-2763-2417"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. Scott Winters","raw_affiliation_strings":["Division of Oncology, Children's Hospital of Philadelphia;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Oncology, Children's Hospital of Philadelphia;","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101817826","display_name":"Peter S. White","orcid":"https://orcid.org/0000-0003-0313-033X"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter S. White","raw_affiliation_strings":["Division of Oncology, Children's Hospital of Philadelphia;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Oncology, Children's Hospital of Philadelphia;","institution_ids":["https://openalex.org/I1335321130"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5106697428"],"corresponding_institution_ids":["https://openalex.org/I1335321130"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.7235,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.68419402,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"20","issue":"4","first_page":"588","last_page":"590"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12388","display_name":"Identification and Quantification in Food","score":0.9940000176429749,"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/T12388","display_name":"Identification and Quantification in Food","score":0.9940000176429749,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.9804999828338623,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9797000288963318,"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/sequence","display_name":"Sequence (biology)","score":0.7423585653305054},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6157056093215942},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5627723932266235},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40623384714126587},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23872536420822144},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21336999535560608}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7423585653305054},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6157056093215942},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5627723932266235},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40623384714126587},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23872536420822144},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21336999535560608}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":"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},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btg466","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg466","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/4/588/48905217/bioinformatics_20_4_588.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:14990458","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14990458","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:CiteSeerX.psu:10.1.1.836.3620","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.836.3620","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/20/4/588.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg466","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg466","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/4/588/48905217/bioinformatics_20_4_588.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/G7496297577","display_name":null,"funder_award_id":"MH60240","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"}],"funders":[{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1984921840","https://openalex.org/W2020573020","https://openalex.org/W2055043387","https://openalex.org/W2084914037","https://openalex.org/W2106538287","https://openalex.org/W2107339893","https://openalex.org/W2122360349","https://openalex.org/W2133403068","https://openalex.org/W2136145671","https://openalex.org/W2142619120","https://openalex.org/W2151549702","https://openalex.org/W2527840914"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"We":[2],"have":[3],"adapted":[4],"the":[5,73,136],"originally":[6],"described":[7],"electronic":[8],"PCR":[9,75],"(e-PCR)":[10],"algorithm":[11],"to":[12,33,38,111,135],"perform":[13],"string":[14],"searches":[15,60],"more":[16,20],"accurately":[17],"and":[18,88,124,129],"much":[19],"rapidly":[21],"than":[22],"previously":[23],"possible.":[24],"Our":[25],"implementation":[26],"[multithreaded":[27],"e-PCR":[28],"(me-PCR)]":[29],"runs":[30],"sufficiently":[31],"fast":[32],"allow":[34],"even":[35],"desktop":[36],"machines":[37],"query":[39],"quickly":[40],"large":[41,45,86],"genomes":[42,110],"with":[43,61],"very":[44],"genomic":[46],"element":[47],"sets.":[48],"In":[49],"addition,":[50],"me-PCR":[51,103,115],"is":[52],"multithreaded,":[53],"interprets":[54],"all":[55],"IUPAC":[56],"nucleotide":[57],"symbols,":[58],"allows":[59],"elements":[62],"specified":[63],"by":[64],"long":[65],"sequences":[66,87],"(such":[67],"as":[68],"SNPs),":[69],"accepts":[70],"ranges":[71],"in":[72,99],"expected":[74],"size":[76],"input":[77],"field,":[78],"requires":[79],"substantially":[80],"less":[81],"memory":[82],"for":[83,108,119],"analysis":[84],"of":[85,92,97],"corrects":[89],"a":[90],"number":[91],"minor":[93],"flaws":[94],"causing":[95],"misreporting":[96],"hits":[98],"exceptional":[100],"cases.":[101],"Thus,":[102],"provides":[104],"increased":[105],"annotation":[106],"capabilities":[107],"complex":[109],"non-expert":[112],"laboratories.":[113],"Availability:":[114],"has":[116],"been":[117],"compiled":[118],"Linux,":[120],"Solaris,":[121],"AIX,":[122],"Windows":[123],"Macintosh":[125],"platforms.":[126],"Both":[127],"source":[128],"executable":[130],"code":[131],"are":[132],"freely":[133],"available":[134],"research":[137],"community":[138],"at":[139],"http://genome.chop.edu/mePCR/":[140]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}