Global or local? Predicting secondary structure and accessibility in mRNAs.

ABSTRACT: Determining the structural properties of mRNA is key to understanding vital post-transcriptional processes. As experimental data on mRNA structure are scarce, accurate structure prediction is required to characterize RNA regulatory mechanisms. Although various structure prediction approaches are available, it is often unclear which to choose and how to set their parameters. Furthermore, no standard measure to compare predictions of local structure exists. We assessed the performance of different methods using two types of data: transcriptome-wide enzymatic probing information and a large, curated set of cis-regulatory elements. To compare the approaches, we introduced structure accuracy, a measure that is applicable to both global and local methods. Our results showed that local folding wa

SUBMITTER: Lange SJ 

PROVIDER: S-EPMC3384308 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature