Fixed-parameter tractable sampling for RNA design with multiple target structures.

ABSTRACT:

Background

The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which substantially reduce the need for costly wet-lab experiments.

Results

We devise a novel approach to a central ingredient of most in-silico design methods: the generation of sequences that fold well into multiple target structures. Based on constraint networks, our approach supports generic Boltzmann-weighted sampling, which enables the positive design of RNA sequences with specific free energies (for each of multiple, possibly pseudoknotted, target structures) and GC-content. Moreover, we study general properties of our approach empirically and generate biologically relevant

SUBMITTER: Hammer S 

PROVIDER: S-EPMC6482512 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature