Methods Mol Biol 2016 ;1404:727-740
Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Phaya Thai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand.
The host microRNA machinery has been employed to control viral replication. To improve safety for live attenuated virus vaccines, the binding sites of the host microRNAs, so-called microRNA response elements (MREs), were incorporated into the virus sequences. These MREs were typically designed for a specific host microRNA and virus sequence with the effectiveness evaluated by experimental trials. Here, we describe a computational flow that can be used to simultaneously design and prioritize the effective MREs in large-scale.