Rastogi Achal, Murik Omer, Bowler Chris, Tirichine Leila
Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, PSL Research University, CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France.
BMC Bioinformatics. 2016 Jul 1;17(1):261. doi: 10.1186/s12859-016-1143-1.
With the emerging interest in phytoplankton research, the need to establish genetic tools for the functional characterization of genes is indispensable. The CRISPR/Cas9 system is now well recognized as an efficient and accurate reverse genetic tool for genome editing. Several computational tools have been published allowing researchers to find candidate target sequences for the engineering of the CRISPR vectors, while searching possible off-targets for the predicted candidates. These tools provide built-in genome databases of common model organisms that are used for CRISPR target prediction. Although their predictions are highly sensitive, the applicability to non-model genomes, most notably protists, makes their design inadequate. This motivated us to design a new CRISPR target finding tool, PhytoCRISP-Ex. Our software offers CRIPSR target predictions using an extended list of phytoplankton genomes and also delivers a user-friendly standalone application that can be used for any genome.
The software attempts to integrate, for the first time, most available phytoplankton genomes information and provide a web-based platform for Cas9 target prediction within them with high sensitivity. By offering a standalone version, PhytoCRISP-Ex maintains an independence to be used with any organism and widens its applicability in high throughput pipelines. PhytoCRISP-Ex out pars all the existing tools by computing the availability of restriction sites over the most probable Cas9 cleavage sites, which can be ideal for mutant screens.
PhytoCRISP-Ex is a simple, fast and accurate web interface with 13 pre-indexed and presently updating phytoplankton genomes. The software was also designed as a UNIX-based standalone application that allows the user to search for target sequences in the genomes of a variety of other species.
随着对浮游植物研究兴趣的不断增加，建立用于基因功能表征的遗传工具变得不可或缺。CRISPR/Cas9系统现已被公认为一种高效且准确的基因组编辑反向遗传工具。已经发表了几种计算工具，使研究人员能够找到用于构建CRISPR载体的候选靶序列，同时搜索预测候选序列的可能脱靶位点。这些工具提供了用于CRISPR靶标预测的常见模式生物的内置基因组数据库。尽管它们的预测高度敏感，但对于非模式基因组，尤其是原生生物的适用性使得它们的设计并不完善。这促使我们设计了一种新的CRISPR靶标查找工具PhytoCRISP-Ex。我们的软件使用扩展的浮游植物基因组列表提供CRISPR靶标预测，并且还提供了一个用户友好的独立应用程序，可用于任何基因组。
该软件首次尝试整合大多数可用的浮游植物基因组信息，并提供一个基于网络的平台，用于在其中以高灵敏度进行Cas9靶标预测。通过提供独立版本，PhytoCRISP-Ex保持了与任何生物体一起使用的独立性，并扩大了其在高通量流程中的适用性。通过计算最可能的Cas9切割位点上限制酶切位点的可用性，PhytoCRISP-Ex超越了所有现有工具，这对于突变体筛选可能是理想的。
PhytoCRISP-Ex是一个简单、快速且准确的网络界面，带有13个预先索引且正在更新的浮游植物基因组。该软件还被设计为基于UNIX的独立应用程序，允许用户在各种其他物种的基因组中搜索靶序列。
