Current deep learning approaches cannot predict RNA secondary structures

Machine learning of RNA structure is more challenging than you might think. Using synthetic data from ViennaRNA's RNAfold to study the capabilities and shortcomings of neural networks for RNA secondary structure prediction in a controlled setting, we argue that shortcomings in the artificial setting will translate to real data.

Posted by Michael T. Wolfinger on . updated

Functional RNA Structures in the 3'UTR of Mosquito-Borne Flaviviruses

The 3'UTR of Mosquito-Borne Flaviviruses (MBFVs) contain evolutionarily conserved functional elements, such as exoribonuclease-resistant RNAs (xrRNAs), dumbbell elements or terminal stem-loops. Here we describe, annotate, and compare these elements within different serological groups of MBFVs.

Posted by Michael T. Wolfinger on . updated

Searching for Telomerase RNAs in Saccharomycetes is TERribly Difficult

Telomerase RNAs are intrinsically difficult to find by homology search methods, even within phylogenetically related groups. This study reports our efforts in annotating telomerase RNAs in the Saccharomycetacea subgroup of yeasts, using the ViennaRNA Package and related tools

Posted by Michael T. Wolfinger on . updated

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