AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms

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.

AutoESDCas: A Web-Based Tool for the Whole-Workflow Editing Sequence Design for Microbial Genome Editing Based on the CRISPR/Cas System

“…15 However, the species, editing types, position of the edited sequence, and technology variants supported by these tools are limited (Table S1). To address these challenges, previously, we developed a web application, AutoESD, 16 which can support whole-workflow ESD for all manipulation types, at any genomic loci, across species and facilitate various SMHR variants (Table S1). Besides SMHR, the CMHR is another typical genome editing technology.…”