Abstract：
Advances in genetic manipulation and genome engineering techniques have enabled on-demand targeted deletion, insertion, and substitution of DNA sequences. One important step in these techniques is the design of editing sequences (e.g. primers, homologous arms) to precisely target and manipulate DNA sequences of interest. Experimental biologists can employ multiple tools in a stepwise manner to assist editing sequence design (ESD), but this requires various software involving non-standardized data exchange and input/output formats. Moreover, necessary quality control steps might be overlooked by non-expert users. This approach is low-throughput and can be error-prone, which illustrates the need for an automated ESD system. In this paper, we introduce AutoESD (https://autoesd.biodesign.ac.cn/), which designs editing sequences for all steps of genetic manipulation of many common homologous-recombination techniques based on screening-markers. Notably, multiple types of manipulations for different targets (CDS or intergenic region) can be processed in one submission. Moreover, AutoESD has an entirely cloud-based serverless architecture, offering high reliability, robustness and scalability which is capable of parallelly processing hundreds of design tasks each having thousands of targets in minutes. To our knowledge, AutoESD is the first cloud platform enabling precise, automated, and high-throughput ESD across species, at any genomic locus for all manipulation types.
摘要：
遗传操作和基因组工程技术的进步已经实现了按需靶向缺失，插入,和DNA序列的替换。这些技术中的一个重要步骤是编辑序列的设计（例如引物，同源臂）以精确靶向和操纵感兴趣的DNA序列。实验生物学家可以逐步使用多种工具来协助编辑序列设计（ESD），但这需要涉及非标准化数据交换和输入/输出格式的各种软件。此外，必要的质量控制步骤可能会被非专家用户忽略。这种方法吞吐量低，并且容易出错，这说明了对自动ESD系统的需求。在本文中,我们介绍AutoESD(https://autoesd.生物设计。AC.cn/),它设计了基于筛选标记的许多常见同源重组技术的遗传操作的所有步骤的编辑序列。值得注意的是,可以在一次提交中处理针对不同靶标(CDS或基因间区域)的多种类型的操作。此外，AutoESD具有完全基于云的无服务器架构，提供高可靠性，健壮性和可扩展性，能够在几分钟内并行处理数百个设计任务，每个任务都有数千个目标。据我们所知,AutoESD是第一个实现精确、自动化,以及跨物种的高通量ESD，在所有操作类型的任何基因组基因座。
