The CRISPR/Cas9 system has recently been developed as a powerful and flexible technology for different purposes of targeted genome engineering, including genome editing (modifying the genome sequence) and gene regulation (without modifying the genome sequence).These applications require design of single guide RNAs (sgRNAs)that are efficient and specific, which, however, remains challenging as it requires consideration of many criteria.Several designer tools have been developed for gene editing, but currently there is no tool to design sgRNAs for gene regulation.With accumulating experimental data on the use of CRISPR/Cas for gene editing and regulation, we implement a comprehensive computational tool based on a set of sgRNA design rules summarized from these published reports.We report a genome-wide sgRNA designer tool and provide an online user-friendly website for predicting sgRNAs that are efficient and specific.We name the tool CRISPR-ERA,for CRISPR-mediated editing, repression, and activation (ERA).