{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T10:58:38Z","timestamp":1753181918761,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,6]],"date-time":"2019-08-06T00:00:00Z","timestamp":1565049600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2018YFC0910504"],"award-info":[{"award-number":["2018YFC0910504"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61732009","61420106009","61622213","B18059"],"award-info":[{"award-number":["61732009","61420106009","61622213","B18059"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hunan Provincial Science and Technology Program","award":["2018WK4001"],"award-info":[{"award-number":["2018WK4001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The recent advance in genome engineering technologies based on CRISPR\/Cas9 system is enabling people to systematically understand genomic functions. A short RNA string (the CRISPR guide RNA) can guide the Cas9 endonuclease to specific locations in complex genomes to cut DNA double-strands. The CRISPR guide RNA is essential for gene editing systems. Recently, the GuideScan software is developed to design CRISPR guide RNA libraries, which can be used for genome editing of coding and non-coding genomic regions effectively. However, GuideScan is a serial program and computationally expensive for designing CRISPR guide RNA libraries from large genomes. Here, we present an efficient guide RNA library designing tool (MultiGuideScan) by implementing multiple processes of GuideScan. MultiGuideScan speeds up the guide RNA library designing about 9\u201312 times on a 32-process mode comparing to GuideScan. MultiGuideScan makes it possible to design guide RNA libraries from large genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation: MultiGuideScan is available at GitHub<\/jats:title>\n                  <jats:p>https:\/\/github.com\/bioinfomaticsCSU\/MultiGuideScan.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz616","type":"journal-article","created":{"date-parts":[[2019,8,5]],"date-time":"2019-08-05T11:13:02Z","timestamp":1565003582000},"page":"920-921","source":"Crossref","is-referenced-by-count":9,"title":["MultiGuideScan: a multi-processing tool for designing CRISPR guide RNA libraries"],"prefix":"10.1093","volume":"36","author":[{"given":"Tao","family":"Li","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , Changsha 410083, China"}]},{"given":"Shaokai","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , Changsha 410083, China"}]},{"given":"Feng","family":"Luo","sequence":"additional","affiliation":[{"name":"School of Computing, Clemson University , Clemson, SC 29634, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4593-9332","authenticated-orcid":false,"given":"Fang-Xiang","family":"Wu","sequence":"additional","affiliation":[{"name":"Division of Biomedical Engineering, Department of Mechanical Engineering, University of Saskatchewan , Saskatoon SKS7N5A9, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1516-0480","authenticated-orcid":false,"given":"Jianxin","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , Changsha 410083, China"}]}],"member":"286","published-online":{"date-parts":[[2019,8,6]]},"reference":[{"key":"2023013110092480500_btz616-B1","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1126\/science.1231143","article-title":"Multiplex genome engineering using CRISPR\/Cas systems","volume":"339","author":"Cong","year":"2013","journal-title":"Science"},{"key":"2023013110092480500_btz616-B2","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1038\/nbt.3437","article-title":"Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9","volume":"34","author":"Doench","year":"2016","journal-title":"Nat. Biotechnol"},{"key":"2023013110092480500_btz616-B3","doi-asserted-by":"crossref","first-page":"1258096.","DOI":"10.1126\/science.1258096","article-title":"The new frontier of genome engineering with CRISPR-Cas9","volume":"346","author":"Doudna","year":"2014","journal-title":"Science"},{"key":"2023013110092480500_btz616-B4","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1038\/nmeth.2812","article-title":"E-CRISP: fast CRISPR target site identification","volume":"11","author":"Heigwer","year":"2014","journal-title":"Nat. Methods"},{"key":"2023013110092480500_btz616-B5","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1038\/nbt.2647","article-title":"DNA targeting specificity of RNA-guided Cas9 nucleases","volume":"31","author":"Hsu","year":"2013","journal-title":"Nat. Biotechnol"},{"key":"2023013110092480500_btz616-B6","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1016\/j.cell.2014.05.010","article-title":"Development and applications of CRISPR-Cas9 for genome engineering","volume":"157","author":"Hsu","year":"2014","journal-title":"Cell"},{"year":"2018","author":"Li","key":"2023013110092480500_btz616-B7"},{"key":"2023013110092480500_btz616-B8","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1038\/nmeth.3543","article-title":"CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo","volume":"12","author":"Moreno-Mateos","year":"2015","journal-title":"Nat. Methods"},{"key":"2023013110092480500_btz616-B9","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nbt.3804","article-title":"GuideScan software for improved single and paired CRISPR guide RNA design","volume":"35","author":"Perez","year":"2017","journal-title":"Nat. Biotechnol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz616\/29200928\/btz616.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/3\/920\/48982389\/bioinformatics_36_3_920.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/3\/920\/48982389\/bioinformatics_36_3_920.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T19:38:42Z","timestamp":1675193922000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/3\/920\/5544268"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,8,6]]},"references-count":9,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2020,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz616","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2020,2,1]]},"published":{"date-parts":[[2019,8,6]]}}}