{"id":"https://openalex.org/W2134023754","doi":"https://doi.org/10.1186/1471-2105-8-18","title":"PILER-CR: Fast and accurate identification of CRISPR repeats","display_name":"PILER-CR: Fast and accurate identification of CRISPR repeats","publication_year":2007,"publication_date":"2007-01-20","ids":{"openalex":"https://openalex.org/W2134023754","doi":"https://doi.org/10.1186/1471-2105-8-18","mag":"2134023754","pmid":"https://pubmed.ncbi.nlm.nih.gov/17239253"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-18","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-18","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/counter/pdf/10.1186/1471-2105-8-18","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077667471","display_name":"R. C. Edgar","orcid":"https://orcid.org/0000-0001-7355-2541"},"institutions":[{"id":"https://openalex.org/I4210097329","display_name":"Tiburon Associates (United States)","ror":"https://ror.org/00wns3e34","country_code":"US","type":"company","lineage":["https://openalex.org/I4210097329"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert C Edgar","raw_affiliation_strings":["bob@drive5.com","Tiburon, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"bob@drive5.com","institution_ids":[]},{"raw_affiliation_string":"Tiburon, USA","institution_ids":["https://openalex.org/I4210097329"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5077667471"],"corresponding_institution_ids":["https://openalex.org/I4210097329"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":3.2709,"has_fulltext":true,"cited_by_count":401,"citation_normalized_percentile":{"value":0.92881366,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"8","issue":"1","first_page":"18","last_page":"18"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.36730000376701355,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.36730000376701355,"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/T10949","display_name":"Genetic Neurodegenerative Diseases","score":0.3409999907016754,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0706000030040741,"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/crispr","display_name":"CRISPR","score":0.8755636215209961},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6750131249427795},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.674003541469574},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6172139048576355},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5368476510047913},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4715673327445984},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.46390125155448914},{"id":"https://openalex.org/keywords/direct-repeat","display_name":"Direct repeat","score":0.4362964630126953},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42036163806915283},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4124915599822998},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25255826115608215},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1942131519317627}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.8755636215209961},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6750131249427795},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.674003541469574},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6172139048576355},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5368476510047913},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4715673327445984},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.46390125155448914},{"id":"https://openalex.org/C29511175","wikidata":"https://www.wikidata.org/wiki/Q5280381","display_name":"Direct repeat","level":4,"score":0.4362964630126953},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42036163806915283},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4124915599822998},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25255826115608215},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1942131519317627},{"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":"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":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","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},{"descriptor_ui":"D019641","descriptor_name":"DNA, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019641","descriptor_name":"DNA, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019641","descriptor_name":"DNA, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-8-18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-18","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-18","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:17239253","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17239253","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:doaj.org/article:429dd61fc13545879e2f1fa40642cd98","is_oa":true,"landing_page_url":"https://doaj.org/article/429dd61fc13545879e2f1fa40642cd98","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 8, Iss 1, p 18 (2007)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1790904","is_oa":true,"landing_page_url":"http://doi.org/10.1186/1471-2105-8-18","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-18","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-18","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":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1495583714","https://openalex.org/W1519266993","https://openalex.org/W1652691445","https://openalex.org/W1986171241","https://openalex.org/W1995867192","https://openalex.org/W1998048394","https://openalex.org/W2024177760","https://openalex.org/W2077190448","https://openalex.org/W2116628377","https://openalex.org/W2122954888","https://openalex.org/W2123965484","https://openalex.org/W2132926880","https://openalex.org/W2153355254","https://openalex.org/W2162049340","https://openalex.org/W2168453028","https://openalex.org/W4239833500"],"related_works":["https://openalex.org/W4293199045","https://openalex.org/W2405656580","https://openalex.org/W3162049976","https://openalex.org/W2642604616","https://openalex.org/W4381712632","https://openalex.org/W3163009052","https://openalex.org/W4365936098","https://openalex.org/W1972626357","https://openalex.org/W2016446927","https://openalex.org/W1971316784"],"abstract_inverted_index":{"BACKGROUND:":[0],"Sequencing":[1],"of":[2,10,21,28,44,69,85,119,137,146,161],"prokaryotic":[3,148],"genomes":[4],"has":[5,125],"recently":[6],"revealed":[7],"the":[8,42,70,81,108,169],"presence":[9],"CRISPR":[11,29,86,139,162],"elements:":[12],"short,":[13],"highly":[14],"conserved":[15],"repeats":[16,30,140],"separated":[17],"by":[18,110,114],"unique":[19],"sequences":[20],"similar":[22],"length.":[23],"The":[24,88,164],"distinctive":[25],"sequence":[26],"signature":[27],"can":[31],"be":[32],"found":[33],"using":[34],"general-purpose":[35],"repeat-":[36],"or":[37],"pattern-finding":[38],"software":[39,165],"tools.":[40],"However,":[41],"output":[43],"such":[45],"tools":[46,64],"is":[47,58,152,166],"not":[48],"always":[49],"ideal":[50],"for":[51,80,156],"studying":[52],"these":[53,120],"repeats,":[54,121],"and":[55,65,83,113,129,159,174],"significant":[56],"effort":[57],"sometimes":[59],"needed":[60],"to":[61,168],"build":[62],"additional":[63],"perform":[66],"manual":[67,111],"analysis":[68,84,145],"output.":[71],"RESULTS:":[72],"We":[73,106,132],"present":[74,134],"PILER-CR,":[75],"a":[76,93,102,135,143,153,175],"program":[77,89],"specifically":[78],"designed":[79],"identification":[82,158],"repeats.":[87,163],"executes":[90],"rapidly,":[91],"completing":[92],"5":[94,99],"Mb":[95],"genome":[96],"in":[97,142],"around":[98],"seconds":[100],"on":[101],"current":[103],"desktop":[104],"computer.":[105],"validate":[107],"algorithm":[109],"curation":[112],"comparison":[115],"with":[116],"published":[117],"surveys":[118],"finding":[122],"that":[123],"PILER-CR":[124,151],"both":[126],"high":[127,130],"sensitivity":[128],"specificity.":[131],"also":[133],"catalogue":[136],"putative":[138],"identified":[141],"comprehensive":[144],"346":[147],"genomes.":[149],"CONCLUSION:":[150],"useful":[154],"tool":[155],"rapid":[157],"classification":[160],"donated":[167],"public":[170],"domain.":[171],"Source":[172],"code":[173],"Linux":[176],"binary":[177],"are":[178],"freely":[179],"available":[180],"at":[181],"http://www.drive5.com/pilercr.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":27},{"year":2024,"cited_by_count":26},{"year":2023,"cited_by_count":29},{"year":2022,"cited_by_count":36},{"year":2021,"cited_by_count":48},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":21},{"year":2018,"cited_by_count":26},{"year":2017,"cited_by_count":37},{"year":2016,"cited_by_count":29},{"year":2015,"cited_by_count":20},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":12}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
