Romero Jazmin, Islam Md Tanvir, Taylor Ryan, Grayson Cathryn, Schoenrock Andrew, Wong Alex
Research Computing Services, Carleton University, Ottawa K1S 5B6, Canada.
Department of Biology, Carleton University, Ottawa K1S 5B6, Canada.
Bioinform Adv. 2022 Sep 27;2(1):vbac069. doi: 10.1093/bioadv/vbac069. eCollection 2022.
Short RNA (sRNA) modulation of gene expression is an increasingly popular tool for bacterial functional genomics. Antisense pairing between an sRNA and a target messenger RNA results in post-transcriptional down-regulation of a specific gene and can thus be used both for investigating individual gene function and for large-scale genetic screens. sRNAs have several advantages over knockout libraries in studies of gene function, including inducibility, the capacity to interrogate essential genes and easy portability to multiple genetic backgrounds. High-throughput, systematic design of antisense RNAs will increase the efficiency and repeatability of sRNA screens. To this end, we present CAREng, the Computer-Automated sRNA Engineer. CAREng designs antisense RNAs for all coding sequences in a given genome, while checking for potential off-targets.
CAREng is available as a Python script and through a web portal (https://caren.carleton.ca).
Supplementary data are available at online.
短RNA（sRNA）对基因表达的调控是细菌功能基因组学中越来越常用的工具。sRNA与靶信使RNA之间的反义配对导致特定基因的转录后下调，因此可用于研究单个基因功能和大规模遗传筛选。在基因功能研究中，sRNA比基因敲除文库具有多个优势，包括可诱导性、研究必需基因的能力以及易于移植到多种遗传背景中。反义RNA的高通量、系统设计将提高sRNA筛选的效率和可重复性。为此，我们推出了CAREng，即计算机自动化sRNA设计工具。CAREng为给定基因组中的所有编码序列设计反义RNA，同时检查潜在的脱靶效应。
CAREng可作为Python脚本通过网络门户（https://caren.carleton.ca）获取。
补充数据可在在线获取。
