{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T00:10:53Z","timestamp":1747181453967,"version":"3.37.3"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2017,7,27]],"date-time":"2017-07-27T00:00:00Z","timestamp":1501113600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31171397","31271533","31301085","81330055","91640119"],"award-info":[{"award-number":["31171397","31271533","31301085","81330055","91640119"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"publisher","award":["Q-1673"],"award-info":[{"award-number":["Q-1673"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The CRISPR\/Cas System has been shown to be an efficient and accurate genome-editing technique. There exist a number of tools to design the guide RNA sequences and predict potential off-target sites. However, most of the existing computational tools on gRNA design are restricted to small deletions. To address this issue, we present pgRNAFinder, with an easy-to-use web interface, which enables researchers to design single or distance-free paired-gRNA sequences. The web interface of pgRNAFinder contains both gRNA search and scoring system. After users input query sequences, it searches gRNA by 3' protospacer-adjacent motif (PAM), and possible off-targets, and scores the conservation of the deleted sequences rapidly. Filters can be applied to identify high-quality CRISPR sites. PgRNAFinder offers gRNA design functionality for 8 vertebrate genomes. Furthermore, to keep pgRNAFinder open, extensible to any organism, we provide the source package for local use.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The pgRNAFinder is freely available at http:\/\/songyanglab.sysu.edu.cn\/wangwebs\/pgRNAFinder\/, and the source code and user manual can be obtained from https:\/\/github.com\/xiexiaowei\/pgRNAFinder.<\/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\/btx472","type":"journal-article","created":{"date-parts":[[2017,7,26]],"date-time":"2017-07-26T17:40:04Z","timestamp":1501090804000},"page":"3642-3644","source":"Crossref","is-referenced-by-count":5,"title":["pgRNAFinder: a web-based tool to design distance independent paired-gRNA"],"prefix":"10.1093","volume":"33","author":[{"given":"Yuanyan","family":"Xiong","sequence":"first","affiliation":[{"name":"Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China"}]},{"given":"Xiaowei","family":"Xie","sequence":"additional","affiliation":[{"name":"Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China"}]},{"given":"Yanzhi","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China"}]},{"given":"Wenbing","family":"Ma","sequence":"additional","affiliation":[{"name":"Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China"}]},{"given":"Puping","family":"Liang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China"}]},{"given":"Zhou","family":"Songyang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China"},{"name":"Cell-Based Assay Screening Core, Baylor College of Medicine, Houston, TX, USA"},{"name":"Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA"},{"name":"Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA"},{"name":"Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, China"}]},{"given":"Zhiming","family":"Dai","sequence":"additional","affiliation":[{"name":"School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, China"},{"name":"Guangdong Province Key Laboratory of Big Data Analysis and Processing, Sun Yat-Sen University, Guangzhou, China"}]}],"member":"286","published-online":{"date-parts":[[2017,7,27]]},"reference":[{"key":"2023051308380789400_btx472-B1","doi-asserted-by":"crossref","first-page":"21312","DOI":"10.1074\/jbc.M114.564625","article-title":"Characterization of genomic deletion efficiency mediated by clustered regularly interspaced palindromic repeats (CRISPR)\/Cas9 nuclease system in mammalian cells","volume":"289","author":"Canver","year":"2014","journal-title":"J. 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