{"id":"https://openalex.org/W2105187403","doi":"https://doi.org/10.1093/bioinformatics/btu114","title":"Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs","display_name":"Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs","publication_year":2014,"publication_date":"2014-02-27","ids":{"openalex":"https://openalex.org/W2105187403","doi":"https://doi.org/10.1093/bioinformatics/btu114","mag":"2105187403","pmid":"https://pubmed.ncbi.nlm.nih.gov/24578404"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu114","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu114","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/13/1805/17140915/btu114.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/30/13/1805/17140915/btu114.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113786545","display_name":"Ambarish Biswas","orcid":null},"institutions":[{"id":"https://openalex.org/I80281795","display_name":"University of Otago","ror":"https://ror.org/01jmxt844","country_code":"NZ","type":"education","lineage":["https://openalex.org/I80281795"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Ambarish Biswas","raw_affiliation_strings":["1 Department of Biochemistry, 2 Department of Microbiology and Immunology and 3 Genetics Otago, University of Otago, Dunedin 9054, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry, 2 Department of Microbiology and Immunology and 3 Genetics Otago, University of Otago, Dunedin 9054, New Zealand","institution_ids":["https://openalex.org/I80281795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035086259","display_name":"Peter C. Fineran","orcid":"https://orcid.org/0000-0002-4639-6704"},"institutions":[{"id":"https://openalex.org/I80281795","display_name":"University of Otago","ror":"https://ror.org/01jmxt844","country_code":"NZ","type":"education","lineage":["https://openalex.org/I80281795"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Peter C. Fineran","raw_affiliation_strings":["1 Department of Biochemistry, 2 Department of Microbiology and Immunology and 3 Genetics Otago, University of Otago, Dunedin 9054, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry, 2 Department of Microbiology and Immunology and 3 Genetics Otago, University of Otago, Dunedin 9054, New Zealand","institution_ids":["https://openalex.org/I80281795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021666366","display_name":"Chris M. Brown","orcid":"https://orcid.org/0000-0003-0079-7067"},"institutions":[{"id":"https://openalex.org/I80281795","display_name":"University of Otago","ror":"https://ror.org/01jmxt844","country_code":"NZ","type":"education","lineage":["https://openalex.org/I80281795"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"Chris M. Brown","raw_affiliation_strings":["1 Department of Biochemistry, 2 Department of Microbiology and Immunology and 3 Genetics Otago, University of Otago, Dunedin 9054, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry, 2 Department of Microbiology and Immunology and 3 Genetics Otago, University of Otago, Dunedin 9054, New Zealand","institution_ids":["https://openalex.org/I80281795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5021666366"],"corresponding_institution_ids":["https://openalex.org/I80281795"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.396,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.80957583,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"30","issue":"13","first_page":"1805","last_page":"1813"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9269000291824341,"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":0.9269000291824341,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.015599999576807022,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.012000000104308128,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/trans-activating-crrna","display_name":"Trans-activating crRNA","score":0.9578638076782227},{"id":"https://openalex.org/keywords/crispr","display_name":"CRISPR","score":0.9229214787483215},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6451175212860107},{"id":"https://openalex.org/keywords/palindrome","display_name":"Palindrome","score":0.5908396244049072},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5449042916297913},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5160779356956482},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4920327365398407},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42637503147125244},{"id":"https://openalex.org/keywords/cas9","display_name":"Cas9","score":0.41402655839920044},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26509904861450195}],"concepts":[{"id":"https://openalex.org/C84356384","wikidata":"https://www.wikidata.org/wiki/Q7833575","display_name":"Trans-activating crRNA","level":5,"score":0.9578638076782227},{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.9229214787483215},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6451175212860107},{"id":"https://openalex.org/C44667518","wikidata":"https://www.wikidata.org/wiki/Q12321","display_name":"Palindrome","level":4,"score":0.5908396244049072},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5449042916297913},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5160779356956482},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4920327365398407},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42637503147125244},{"id":"https://openalex.org/C132455925","wikidata":"https://www.wikidata.org/wiki/Q16965677","display_name":"Cas9","level":4,"score":0.41402655839920044},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26509904861450195}],"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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btu114","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu114","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/13/1805/17140915/btu114.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:24578404","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24578404","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu114","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu114","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/13/1805/17140915/btu114.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":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1525072270","https://openalex.org/W1543796220","https://openalex.org/W1556779005","https://openalex.org/W1572955611","https://openalex.org/W1577973179","https://openalex.org/W1597185777","https://openalex.org/W1966021055","https://openalex.org/W1967046461","https://openalex.org/W1969479889","https://openalex.org/W1986718765","https://openalex.org/W1989568784","https://openalex.org/W1998661584","https://openalex.org/W2000545911","https://openalex.org/W2004311938","https://openalex.org/W2013018092","https://openalex.org/W2015555968","https://openalex.org/W2017685660","https://openalex.org/W2044167113","https://openalex.org/W2050059115","https://openalex.org/W2053019594","https://openalex.org/W2063148079","https://openalex.org/W2064425325","https://openalex.org/W2071195434","https://openalex.org/W2071795036","https://openalex.org/W2072051684","https://openalex.org/W2073059496","https://openalex.org/W2086860427","https://openalex.org/W2095624846","https://openalex.org/W2097379120","https://openalex.org/W2108101601","https://openalex.org/W2123948195","https://openalex.org/W2127391962","https://openalex.org/W2131157113","https://openalex.org/W2134023754","https://openalex.org/W2134941170","https://openalex.org/W2137721714","https://openalex.org/W2138116029","https://openalex.org/W2148245360","https://openalex.org/W2149594762","https://openalex.org/W2149635735","https://openalex.org/W2149751339","https://openalex.org/W2153173493","https://openalex.org/W2153537688","https://openalex.org/W2153650494","https://openalex.org/W2159207970","https://openalex.org/W2163241233","https://openalex.org/W2163481728","https://openalex.org/W2163723712","https://openalex.org/W2165011752"],"related_works":["https://openalex.org/W2022419379","https://openalex.org/W1690029344","https://openalex.org/W3195673132","https://openalex.org/W4378347774","https://openalex.org/W4220960485","https://openalex.org/W3146454725","https://openalex.org/W2140658947","https://openalex.org/W2317788533","https://openalex.org/W2947638201","https://openalex.org/W2564226239"],"abstract_inverted_index":{"MOTIVATION:":[0],"CRISPR":[1,90,118,129],"RNAs":[2],"(crRNAs)":[3],"are":[4,67,125,136],"a":[5,13,162],"type":[6],"of":[7,16,32,38,51,89,95,109,159,161,165],"small":[8],"non-coding":[9],"RNA":[10],"that":[11,72,104,124],"form":[12],"key":[14],"part":[15],"an":[17,102],"acquired":[18],"immune":[19],"system":[20],"in":[21,29],"prokaryotes.":[22],"Specific":[23],"prediction":[24,142],"methods":[25],"find":[26],"crRNA-encoding":[27],"loci":[28,91],"nearly":[30],"half":[31],"sequenced":[33],"bacterial,":[34],"and":[35,132],"three":[36],"quarters":[37],"archaeal,":[39],"species.":[40],"These":[41],"Clustered":[42],"Regularly":[43],"Interspaced":[44],"Short":[45],"Palindromic":[46],"Repeats":[47],"(CRISPR)":[48],"arrays":[49],"consist":[50],"repeat":[52,119,130],"elements":[53],"alternating":[54],"with":[55,75],"specific":[56],"spacers.":[57],"Generally":[58],"one":[59],"strand":[60,108],"is":[61,151,174],"transcribed,":[62],"producing":[63],"long":[64],"pre-crRNAs,":[65],"which":[66,135],"processed":[68],"to":[69,79],"short":[70],"crRNAs":[71],"base":[73],"pair":[74],"invading":[76],"nucleic":[77],"acids":[78],"facilitate":[80],"their":[81],"destruction.":[82],"No":[83],"current":[84],"software":[85],"for":[86],"the":[87,93,107,110,128,157],"discovery":[88],"predicts":[92,106],"direction":[94],"crRNA":[96],"transcription.":[97],"RESULTS:":[98],"We":[99],"have":[100],"developed":[101],"algorithm":[103],"accurately":[105],"resulting":[111],"crRNAs.":[112],"The":[113,141,170],"method":[114],"uses":[115,122],"as":[116],"input":[117],"predictions.":[120],"CRISPRDirection":[121,154],"parameters":[123],"calculated":[126],"from":[127,177],"predictions":[131],"flanking":[133],"sequences,":[134],"combined":[137],"by":[138],"weighted":[139],"voting.":[140],"may":[143],"use":[144],"prior":[145],"coding":[146],"sequence":[147],"annotation":[148],"but":[149],"this":[150],"not":[152],"required.":[153],"correctly":[155],"predicted":[156],"orientation":[158],"94%":[160],"reference":[163],"set":[164],"arrays.":[166],"AVAILABILITY":[167],"AND":[168],"IMPLEMENTATION:":[169],"Perl":[171],"source":[172],"code":[173],"freely":[175],"available":[176],"http://bioanalysis.otago.ac.nz/CRISPRDirection.":[178]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
