Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.

ABSTRACT: Recently, several experimental techniques have emerged for probing RNA structures based on high-throughput sequencing. However, most secondary structure prediction tools that incorporate probing data are designed and optimized for particular types of experiments. For example, RNAstructure-Fold is optimized for SHAPE data, while SeqFold is optimized for PARS data. Here, we report a new RNA secondary structure prediction method, restrained MaxExpect (RME), which can incorporate multiple types of experimental probing data and is based on a free energy model and an MEA (maximizing expected accuracy) algorithm. We first demonstrated that RME substantially improved secondary structure prediction with perfect restraints (base pair information of known structures). Next, we collected structure-pro

SUBMITTER: Wu Y 

PROVIDER: S-EPMC4551937 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature