{"id":"https://openalex.org/W4296777504","doi":"https://doi.org/10.1093/bioinformatics/btac466","title":"CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection","display_name":"CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection","publication_year":2022,"publication_date":"2022-09-01","ids":{"openalex":"https://openalex.org/W4296777504","doi":"https://doi.org/10.1093/bioinformatics/btac466","pmid":"https://pubmed.ncbi.nlm.nih.gov/36124799"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac466","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac466","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btac466","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104249767","display_name":"Alexander Mitrofanov","orcid":"https://orcid.org/0000-0002-9289-6726"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alexander Mitrofanov","raw_affiliation_strings":["Chair of Bioinformatics, University of Freiburg , Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chair of Bioinformatics, University of Freiburg , Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073784729","display_name":"Marcus Ziemann","orcid":"https://orcid.org/0000-0002-2718-9048"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marcus Ziemann","raw_affiliation_strings":["Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg , Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg , Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008400965","display_name":"Omer S. Alkhnbashi","orcid":"https://orcid.org/0000-0001-8088-590X"},"institutions":[{"id":"https://openalex.org/I134085113","display_name":"King Fahd University of Petroleum and Minerals","ror":"https://ror.org/03yez3163","country_code":"SA","type":"education","lineage":["https://openalex.org/I134085113"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Omer S Alkhnbashi","raw_affiliation_strings":["Information and Computer Science Department, King Fahd University of Petroleum and Minerals , Dhahran, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information and Computer Science Department, King Fahd University of Petroleum and Minerals , Dhahran, Saudi Arabia","institution_ids":["https://openalex.org/I134085113"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089148815","display_name":"Wolfgang R. Hess","orcid":"https://orcid.org/0000-0002-5340-3423"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Wolfgang R Hess","raw_affiliation_strings":["Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg , Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg , Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017672883","display_name":"Rolf Backofen","orcid":"https://orcid.org/0000-0001-8231-3323"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Rolf Backofen","raw_affiliation_strings":["Chair of Bioinformatics, University of Freiburg , Freiburg, Germany","Signalling Research Centres BIOSS and CIBSS, University of Freiburg , Freiburg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8231-3323","affiliations":[{"raw_affiliation_string":"Chair of Bioinformatics, University of Freiburg , Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg , Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5008400965","https://openalex.org/A5017672883"],"corresponding_institution_ids":["https://openalex.org/I134085113","https://openalex.org/I161046081"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.386,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.80839527,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"38","issue":"Supplement_2","first_page":"ii42","last_page":"ii48"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9735999703407288,"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":0.9735999703407288,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.003000000026077032,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant 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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0017000000225380063,"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":0.8952938318252563},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.675165057182312},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41909319162368774},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22506728768348694},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11162945628166199},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08034726977348328}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.8952938318252563},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.675165057182312},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41909319162368774},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22506728768348694},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11162945628166199},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08034726977348328}],"mesh":[{"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"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":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac466","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac466","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36124799","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36124799","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:pubmedcentral.nih.gov:9486595","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9486595","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac466","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac466","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2744454249","display_name":null,"funder_award_id":"BA 2168/23-1/2","funder_id":"https://openalex.org/F4320308022","funder_display_name":"California Department of Fish and Game"},{"id":"https://openalex.org/G4648121172","display_name":null,"funder_award_id":"SPP 2141","funder_id":"https://openalex.org/F4320308022","funder_display_name":"California Department of Fish and Game"},{"id":"https://openalex.org/G4988255525","display_name":null,"funder_award_id":"ECCB2022","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5207692089","display_name":null,"funder_award_id":"HE 2544/14-2","funder_id":"https://openalex.org/F4320308022","funder_display_name":"California Department of Fish and Game"}],"funders":[{"id":"https://openalex.org/F4320308022","display_name":"California Department of Fish and Game","ror":"https://ror.org/02v6w2r95"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321421","display_name":"Albert-Ludwigs-Universit\u00e4t Freiburg","ror":"https://ror.org/0245cg223"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1976765586","https://openalex.org/W1988101725","https://openalex.org/W1993521195","https://openalex.org/W2021134519","https://openalex.org/W2055043387","https://openalex.org/W2059363769","https://openalex.org/W2076785026","https://openalex.org/W2124812694","https://openalex.org/W2124995041","https://openalex.org/W2131462431","https://openalex.org/W2135689945","https://openalex.org/W2142515819","https://openalex.org/W2156125289","https://openalex.org/W2160378127","https://openalex.org/W2610733803","https://openalex.org/W2766354636","https://openalex.org/W2948927976","https://openalex.org/W2991913838","https://openalex.org/W2995081665","https://openalex.org/W3031943262","https://openalex.org/W3036373230","https://openalex.org/W3096886392","https://openalex.org/W3111496797","https://openalex.org/W3139184535","https://openalex.org/W3167995117","https://openalex.org/W3174748198","https://openalex.org/W3183749267","https://openalex.org/W3194106878","https://openalex.org/W3194674995","https://openalex.org/W3214141913"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4293199045","https://openalex.org/W2405656580","https://openalex.org/W2642604616","https://openalex.org/W3162049976","https://openalex.org/W4381712632","https://openalex.org/W3163009052","https://openalex.org/W4213036952","https://openalex.org/W4377030018","https://openalex.org/W3111496797"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,112,204],"CRISPR-Cas9":[2],"system":[3,9],"is":[4,114,191,209],"a":[5,33,48,88,115,124],"Type":[6,198],"II":[7,178],"CRISPR":[8,70,83,150,179,185],"that":[10,37],"has":[11],"rapidly":[12],"become":[13],"the":[14,28,39,43,46,72,77,109,136,141,145,149,154,157,172,175,192,207,215,230],"most":[15],"versatile":[16],"and":[17,32,57,69,94,144,153,181],"widespread":[18],"tool":[19,190],"for":[20,53,64,92,140,194,197],"genome":[21],"engineering.":[22],"It":[23],"consists":[24],"of":[25,74,96,108,127,156,206],"two":[26],"components,":[27],"Cas9":[29,176],"effector":[30,67,187],"protein,":[31],"single":[34],"guide":[35],"RNA":[36,51],"combines":[38,103],"spacer":[40],"(for":[41],"identifying":[42],"target)":[44],"with":[45],"tracrRNA,":[47],"trans-activating":[49],"small":[50],"required":[52],"both":[54],"crRNA":[55],"maturation":[56],"interference.":[58],"While":[59],"there":[60],"are":[61,160,240],"well-established":[62],"methods":[63],"screening":[65,93],"Cas":[66],"proteins":[68],"arrays,":[71],"detection":[73],"tracrRNA":[75,97,142,196],"remains":[76],"bottleneck":[78],"in":[79,99,221],"detecting":[80,195],"Class":[81],"2":[82],"systems.":[84,200],"RESULTS:":[85],"We":[86],"introduce":[87],"new":[89],"pipeline":[90,102],"CRISPRtracrRNA":[91,208],"evaluation":[95],"candidates":[98],"genomes.":[100],"This":[101],"evidence":[104],"from":[105,123],"different":[106],"components":[107],"Cas9-sgRNA":[110],"complex.":[111],"core":[113],"newly":[116],"developed":[117],"structural":[118],"model":[119],"via":[120,162],"covariance":[121],"models":[122],"sequence-structure":[125],"alignment":[126],"experimentally":[128],"validated":[129],"tracrRNAs.":[130],"As":[131],"additional":[132],"evidence,":[133,169],"we":[134,170],"determine":[135],"terminator":[137],"signal":[138],"(required":[139],"transcription)":[143],"RNA-RNA":[146],"interaction":[147],"between":[148],"array":[151],"repeat":[152],"5'-part":[155],"tracrRNA.":[158],"Repeats":[159],"detected":[161],"an":[163],"ML-based":[164],"approach":[165],"(CRISPRidenify).":[166],"Providing":[167],"further":[168],"detect":[171],"cassette":[173],"containing":[174],"(Type":[177,183],"systems)":[180,186],"Cas12":[182],"V":[184,199],"protein.":[188],"Our":[189],"first":[193],"AVAILABILITY":[201],"AND":[202],"IMPLEMENTATION:":[203],"implementation":[205],"available":[210,241],"on":[211],"GitHub":[212],"upon":[213,227],"requesting":[214],"access":[216],"permission,":[217],"(https://github.com/BackofenLab/CRISPRtracrRNA).":[218],"Data":[219],"generated":[220],"this":[222],"study":[223],"can":[224],"be":[225],"obtained":[226],"request":[228],"to":[229],"corresponding":[231],"person:":[232],"Rolf":[233],"Backofen":[234],"(backofen@informatik.uni-freiburg.de).":[235],"SUPPLEMENTARY":[236],"INFORMATION:":[237],"Supplementary":[238],"data":[239],"at":[242],"Bioinformatics":[243],"online.":[244]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
