{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T07:35:07Z","timestamp":1775979307997,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2017,1,19]],"date-time":"2017-01-19T00:00:00Z","timestamp":1484784000000},"content-version":"vor","delay-in-days":148,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Korea Healthcare technology R&D Project, Ministry for Health & Welfare Affairs","award":["HI16C1012"],"award-info":[{"award-number":["HI16C1012"]}]},{"name":"S.B. and Institute for Basic Science","award":["IBS-R021-D1"],"award-info":[{"award-number":["IBS-R021-D1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Genome editing with programmable nucleases has been widely adopted in research and medicine. Next generation sequencing (NGS) platforms are now widely used for measuring the frequencies of mutations induced by CRISPR-Cas9 and other programmable nucleases. Here, we present an online tool, Cas-Analyzer, a JavaScript-based implementation for NGS data analysis. Because Cas-Analyzer is completely used at a client-side web browser on-the-fly, there is no need to upload very large NGS datasets to a server, a time-consuming step in genome editing analysis. Currently, Cas-Analyzer supports various programmable nucleases, including single nucleases and paired nucleases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Free access at http:\/\/www.rgenome.net\/cas-analyzer\/.<\/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\/btw561","type":"journal-article","created":{"date-parts":[[2016,8,25]],"date-time":"2016-08-25T02:49:07Z","timestamp":1472093347000},"page":"286-288","source":"Crossref","is-referenced-by-count":395,"title":["Cas-analyzer: an online tool for assessing genome editing results using NGS data"],"prefix":"10.1093","volume":"33","author":[{"given":"Jeongbin","family":"Park","sequence":"first","affiliation":[{"name":"Department of Chemistry, Hanyang University, Seoul, South Korea"}]},{"given":"Kayeong","family":"Lim","sequence":"additional","affiliation":[{"name":"Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea"},{"name":"Department of Chemistry, Seoul National University, Seoul, South Korea"}]},{"given":"Jin-Soo","family":"Kim","sequence":"additional","affiliation":[{"name":"Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea"},{"name":"Department of Chemistry, Seoul National University, Seoul, South Korea"}]},{"given":"Sangsu","family":"Bae","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Hanyang University, Seoul, South Korea"},{"name":"Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea"}]}],"member":"286","published-online":{"date-parts":[[2016,8,24]]},"reference":[{"key":"2023020204303007900_btw561-B1","doi-asserted-by":"crossref","first-page":"30620","DOI":"10.1038\/srep30620","article-title":"DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins","volume":"6","author":"Baek","year":"2016","journal-title":"Sci. Rep"},{"key":"2023020204303007900_btw561-B2","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1038\/nbt.2507","article-title":"Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease","volume":"31","author":"Cho","year":"2013","journal-title":"Nat. Biotechnol"},{"key":"2023020204303007900_btw561-B3","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1101\/gr.162339.113","article-title":"Analysis of off-target effects of CRISPR\/Cas-derived RNAguided endonucleases and nickases","volume":"24","author":"Cho","year":"2014","journal-title":"Genome Res"},{"key":"2023020204303007900_btw561-B4","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":"2023020204303007900_btw561-B5","doi-asserted-by":"crossref","first-page":"2968","DOI":"10.1093\/bioinformatics\/btu427","article-title":"Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA)","volume":"30","author":"G\u00fcell","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020204303007900_btw561-B6","doi-asserted-by":"crossref","first-page":"15644","DOI":"10.1073\/pnas.1313587110","article-title":"Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis","volume":"110","author":"Hou","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020204303007900_btw561-B7","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1038\/nbt.3596","article-title":"Targeted mutagenesis in mice by electroporation of Cpf1 ribo nucleoproteins","volume":"34","author":"Hur","year":"2016","journal-title":"Nat. Biotechnol"},{"key":"2023020204303007900_btw561-B24"},{"key":"2023020204303007900_btw561-B8","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1038\/nbt.3609","article-title":"Genome-wide analysis reveals specificities of Cpf1 endonucle ases in human cells","volume":"34","author":"Kim","year":"2016","journal-title":"Nat. Biotechnol"},{"key":"2023020204303007900_btw561-B9","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1101\/gr.089417.108","article-title":"Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly","volume":"19","author":"Kim","year":"2009","journal-title":"Genome Res"},{"key":"2023020204303007900_btw561-B10","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/nrg3686","article-title":"A guide to genome engineering with programmable nucleases","volume":"15","author":"Kim","year":"2014","journal-title":"Nat. Rev. Genet"},{"key":"2023020204303007900_btw561-B11","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1038\/nbt.3614","article-title":"Generation of knockout mice by Cpf1-mediated gene targeting","volume":"34","author":"Kim","year":"2016","journal-title":"Nat. Biotechnol"},{"key":"2023020204303007900_btw561-B12","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1038\/nature16526","article-title":"High-fidelity CRISPR\u2013Cas9 nucleases with no detectable genome-wide off-target effects","volume":"529","author":"Kleinstiver","year":"2016","journal-title":"Nature"},{"key":"2023020204303007900_btw561-B25"},{"key":"2023020204303007900_btw561-B13","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1126\/science.aad5143","article-title":"In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy","volume":"351","author":"Nelson","year":"2016","journal-title":"Science"},{"key":"2023020204303007900_btw561-B14","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1038\/nbt1410","article-title":"Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases","volume":"26","author":"Perez","year":"2008","journal-title":"Nat. Biotechnol"},{"key":"2023020204303007900_btw561-B15","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/nbt.3583","article-title":"Analyzing CRISPR genome-editing experiments with CRISPResso","volume":"34","author":"Pinello","year":"2016","journal-title":"Nat. Biotechnol"},{"key":"2023020204303007900_btw561-B16","doi-asserted-by":"crossref","first-page":"1380","DOI":"10.1016\/j.cell.2013.08.021","article-title":"Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity","volume":"154","author":"Ran","year":"2013","journal-title":"Cell"},{"key":"2023020204303007900_btw561-B17","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/nature14299","article-title":"In vivo genome editing using Staphylococcus aureus Cas9","volume":"520","author":"Ran","year":"2015","journal-title":"Nature"},{"key":"2023020204303007900_btw561-B18","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","article-title":"EMBOSS: the European Molecular Biology Open Software Suite","volume":"16","author":"Rice","year":"2000","journal-title":"Trends Genet"},{"key":"2023020204303007900_btw561-B19","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1126\/science.aad5227","article-title":"Rationally engineered Cas9 nucleases with improved specificity","volume":"351","author":"Slaymaker","year":"2016","journal-title":"Science"},{"key":"2023020204303007900_btw561-B20","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/nbt.2908","article-title":"Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing","volume":"32","author":"Tsai","year":"2014","journal-title":"Nat. Biotechnol"},{"key":"2023020204303007900_btw561-B21","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1016\/j.molp.2015.06.001","article-title":"AGEseq: analysis of genome editing by sequencing","volume":"8","author":"Xue","year":"2015","journal-title":"Mol. Plant"},{"key":"2023020204303007900_btw561-B22","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1016\/j.cell.2015.09.038","article-title":"Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System","volume":"163","author":"Zetsche","year":"2015","journal-title":"Cell"},{"key":"2023020204303007900_btw561-B23","doi-asserted-by":"crossref","first-page":"6420","DOI":"10.1038\/srep06420","article-title":"An efficient genotyping method for genome-modified animals and human cells generated with CRISPR\/Cas9 system","volume":"4","author":"Zhu","year":"2014","journal-title":"Sci. Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/2\/286\/49037148\/bioinformatics_33_2_286.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/2\/286\/49037148\/bioinformatics_33_2_286.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:31:00Z","timestamp":1675312260000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/2\/286\/2525673"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2016,8,24]]},"references-count":25,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2017,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw561","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,1,15]]},"published":{"date-parts":[[2016,8,24]]}}}