Exploring the RNA folding energy landscape using scalable distributed cyberinfrastructure

The increasing significance of RNAs in transcriptional or post-transcriptional gene regulation processes has generated considerable interest towards the prediction of RNA folding and its sensitivity to environmental factors. We use Boltzmann-weighted sampling to generate RNA secondary structures, which are used to characterize the energy landscape, via the distributions of energies and base-pair distances. Depending upon the length of an RNA, the number of sequences investigated, and the sample size of generated structures -- generating and analyzing sufficient samples can be computationally challenging. We introduce and develop a lightweight and extensible runtime environment that is effective across a range of RNA sizes and other parameters, as well as over a range of infrastructure

• Type: Conference
• Year: 2010
• Where: HPDC
• Authors: Joohyun Kim, Wei Huang, Sharath Maddineni, Fareed Aboul-Ela, Shantenu Jha
• Keywords: Distributed And Parallel Computing, Energy Landscapes, HPDC 2010, RNA Folding, RNA Secondary Structures