A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.

ABSTRACT:

Motivations

The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity.

Results

In this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nu

SUBMITTER: Reinharz V 

PROVIDER: S-EPMC3694657 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature