TBI-p-2016-2

Titel:
RNAblueprint: Flexible and universal multiple target nucleic acid sequence design

Author(s):
Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker and Sven Findeiß

submitted to:

Abstract:
Motivation: Realizing the value of synthetic biology in biotechnology and medicine re- quires the design of molecules with specialized functions. Due to its close structure to function relationship, and the availability of good structure prediction methods and energy models, RNA is perfectly suited to be synthetically engineered with predefined properties. However, currently available RNA design tools cannot be easily adapted to accommodate new design specifications. Furthermore, complicated sampling and optimization methods are often developed to suit a specific RNA design goal, adding to their inflexibility. Results: We developed a C++ library implementing a graph coloring approach to uniformly sample sequences compatible with structural and sequence constraints from the typically very large solution space. Uniform sampling from the solution space not only makes optimization runs much more performant, but also raises the probability of finding better solutions for long optimization runs. We show that our software can be combined with any other software pack- age to allow diverse RNA design applications. Scripting interfaces allow the easy adaption of existing code to accommodate new scenarios, making the whole design process universal and flexible. We implemented example design approaches written in Python to demonstrate the advantages of a scripting language in conjunction with the RNAblueprint library for sequence sampling.

Link to publication:

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