{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T07:50:05Z","timestamp":1782892205041,"version":"3.54.5"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2021,5,3]],"date-time":"2021-05-03T00:00:00Z","timestamp":1620000000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010446","name":"Institute for Basic Science","doi-asserted-by":"publisher","award":["IBS-R021-D1"],"award-info":[{"award-number":["IBS-R021-D1"]}],"id":[{"id":"10.13039\/501100010446","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2021M3A9H3015389"],"award-info":[{"award-number":["2021M3A9H3015389"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003661","name":"Korea Institute for Advancement of Technology","doi-asserted-by":"publisher","award":["P0015362"],"award-info":[{"award-number":["P0015362"]}],"id":[{"id":"10.13039\/501100003661","id-type":"DOI","asserted-by":"publisher"}]},{"name":"New Breeding Technologies Development Program","award":["PJ01487401202001"],"award-info":[{"award-number":["PJ01487401202001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Prime editing technology is capable of generating targeted insertions, deletions, and base conversions. However, the process of designing prime editing guide RNAs (pegRNAs), which contain a primer binding site and a reverse-transcription template at the 3\u2032 end, is more complex than that for the single guide RNAs used with CRISPR nucleases or base editors. Furthermore, the assessment of high-throughput sequencing data after prime editors (PEs) have been employed should consider the unique feature of PEs; thus, pre-existing assessment tools cannot directly be adopted for PEs. Here, we present two user-friendly web-based tools for PEs, named PE-Designer and PE-Analyzer. PE-Designer, a dedicated tool for pegRNA selection, provides all possible target sequences, pegRNA extension sequences, and nicking guide RNA sequences together with useful information, and displays the results in an interactive image. PE-Analyzer, a dedicated tool for PE outcome analysis, accepts high-throughput sequencing data, summarizes mutation-related information in a table, and provides interactive graphs. PE-Analyzer was mainly written using JavaScript so that it can analyze several data sets without requiring that huge sequencing data (&amp;gt;100MB) be uploaded to the server, reducing analysis time and increasing personal security. PE-Designer and PE-Analyzer are freely available at http:\/\/www.rgenome.net\/pe-designer\/ and http:\/\/www.rgenome.net\/pe-analyzer\/ without a login process.<\/jats:p>","DOI":"10.1093\/nar\/gkab319","type":"journal-article","created":{"date-parts":[[2021,4,22]],"date-time":"2021-04-22T02:41:56Z","timestamp":1619059316000},"page":"W499-W504","source":"Crossref","is-referenced-by-count":108,"title":["PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing"],"prefix":"10.1093","volume":"49","author":[{"given":"Gue-Ho","family":"Hwang","sequence":"first","affiliation":[{"name":"Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"You Kyeong","family":"Jeong","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omer","family":"Habib","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sung-Ah","family":"Hong","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kayeong","family":"Lim","sequence":"additional","affiliation":[{"name":"Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin-Soo","family":"Kim","sequence":"additional","affiliation":[{"name":"Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea"},{"name":"Department of Chemistry, Seoul National University, Seoul, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3615-8566","authenticated-orcid":false,"given":"Sangsu","family":"Bae","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,5,3]]},"reference":[{"key":"2021070812043497300_B1","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1016\/j.stem.2013.10.016","article-title":"Correction of a genetic disease in mouse via use of CRISPR\u2013Cas9","volume":"13","author":"Wu","year":"2013","journal-title":"Cell Stem Cell"},{"key":"2021070812043497300_B2","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1016\/j.molp.2016.01.001","article-title":"Engineering Herbicide-Resistant Rice Plants through CRISPR\/Cas9-Mediated homologous recombination of acetolactate synthase","volume":"9","author":"Sun","year":"2016","journal-title":"Mol Plant"},{"key":"2021070812043497300_B3","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1016\/j.cell.2014.05.010","article-title":"Development and applications of CRISPR\u2013Cas9 for genome engineering","volume":"157","author":"Hsu","year":"2014","journal-title":"Cell"},{"key":"2021070812043497300_B4","doi-asserted-by":"crossref","first-page":"1258096","DOI":"10.1126\/science.1258096","article-title":"Genome editing. The new frontier of genome engineering with CRISPR\u2013Cas9","volume":"346","author":"Doudna","year":"2014","journal-title":"Science"},{"key":"2021070812043497300_B5","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nbt.2842","article-title":"CRISPR-Cas systems for editing, regulating and targeting genomes","volume":"32","author":"Sander","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2021070812043497300_B6","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1016\/j.cell.2014.02.001","article-title":"Crystal structure of Cas9 in complex with guide RNA and target DNA","volume":"156","author":"Nishimasu","year":"2014","journal-title":"Cell"},{"key":"2021070812043497300_B7","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1126\/science.1225829","article-title":"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity","volume":"337","author":"Jinek","year":"2012","journal-title":"Science"},{"key":"2021070812043497300_B8","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. 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Biotechnol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/W1\/W499\/38842158\/gkab319.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/W1\/W499\/38842158\/gkab319.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,2]],"date-time":"2023-11-02T14:23:56Z","timestamp":1698935036000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/49\/W1\/W499\/6262559"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,3]]},"references-count":38,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2021,5,3]]},"published-print":{"date-parts":[[2021,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab319","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,7,2]]},"published":{"date-parts":[[2021,5,3]]}}}