Developing complex RNA design applications in the Infrared framework - Archive ouverte HAL
Chapitre D'ouvrage Année : 2022

Developing complex RNA design applications in the Infrared framework

Résumé

Applications in biotechnology and bio-medical research call for effective strategies to design novel RNAs with very specific properties. Such advanced design tasks require support by computational design tools but at the same time put high demands on their flexibility and expressivity to model the applications-specific requirements. To address such demands, we present the computational framework Infrared. It supports developing advanced customized design tools, which generate RNA sequences with specific properties, often in a few lines of Python code. This text guides the reader in tutorial-format through the development of complex design applications. Thanks to the declarative, compositional approach of Infrared, we can describe this development as step-by-step extension of an elementary design task. Thus, we start with generating sequences that are compatible with a single RNA structure and go all the way to RNA design targeting complex positive and negative design objectives with respect to single or even multiple target structures. Finally, we present a 'real-world' application of computational RNA design of a biotechnological device. We use Infrared to generate design candidates of an artificial AND-riboswitch, which could activate gene expression (only) in the simultaneous presence of two different metabolites.
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Dates et versions

hal-03711828 , version 1 (01-07-2022)
hal-03711828 , version 2 (16-11-2022)

Identifiants

  • HAL Id : hal-03711828 , version 1

Citer

Hua-Ting Yao, Yann Ponty, Sebastian Will. Developing complex RNA design applications in the Infrared framework. RNA Folding - Methods and Protocols, 2022. ⟨hal-03711828v1⟩
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