TBI-p-2014-7

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Titel:
Memory efficient RNA energy landscape exploration

Author(s):
Martin Mann, Marcel Kucharík, Christoph Flamm and Michael T. Wolfinger

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Abstract:
Motivation: Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems, however they are still restricted by huge memory requirements of exact approaches. Results: We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models with highly reduced memory requirements. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, we demonstrate the need for exact transition models by comparing two barrier-based appoaches and perform a detailed investigation of gradient basins in RNA energy landscapes. Availability: Source code is part of the C++ Energy Landscape Library available at http://www.bioinf.uni-freiburg.de/Software/. Contact: mmann@informatik.uni-freiburg.de

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