CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments

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CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments

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Title: CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments
Author: Cao, Qingyi; Ma, Jian; Chen, Chen-Hao; Xu, Han; Chen, Zhi; Li, Wei; Liu, X. Shirley

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Citation: Cao, Qingyi, Jian Ma, Chen-Hao Chen, Han Xu, Zhi Chen, Wei Li, and X. Shirley Liu. 2017. “CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments.” PLoS ONE 12 (9): e0184281. doi:10.1371/journal.pone.0184281.
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Abstract: The recently developed CRISPR screen technology, based on the CRISPR/Cas9 genome editing system, enables genome-wide interrogation of gene functions in an efficient and cost-effective manner. Although many computational algorithms and web servers have been developed to design single-guide RNAs (sgRNAs) with high specificity and efficiency, algorithms specifically designed for conducting CRISPR screens are still lacking. Here we present CRISPR-FOCUS, a web-based platform to search and prioritize sgRNAs for CRISPR screen experiments. With official gene symbols or RefSeq IDs as the only mandatory input, CRISPR-FOCUS filters and prioritizes sgRNAs based on multiple criteria, including efficiency, specificity, sequence conservation, isoform structure, as well as genomic variations including Single Nucleotide Polymorphisms and cancer somatic mutations. CRISPR-FOCUS also provides pre-defined positive and negative control sgRNAs, as well as other necessary sequences in the construct (e.g., U6 promoters to drive sgRNA transcription and RNA scaffolds of the CRISPR/Cas9). These features allow users to synthesize oligonucleotides directly based on the output of CRISPR-FOCUS. Overall, CRISPR-FOCUS provides a rational and high-throughput approach for sgRNA library design that enables users to efficiently conduct a focused screen experiment targeting up to thousands of genes. (CRISPR-FOCUS is freely available at
Published Version: doi:10.1371/journal.pone.0184281
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