Abstract
BackgroundIt is known that functional RNAs often switch their functions by forming different secondary structures. Popular tools for RNA secondary structures prediction, however, predict the single ‘best’ structures, and do not produce alternative structures. There are bioinformatics tools to predict suboptimal structures, but it is difficult to detect which alternative secondary structures are essential.ResultsWe proposed a new computational method to detect essential alternative secondary structures from RNA sequences by decomposing the base-pairing probability matrix. The decomposition is calculated by a newly implemented software tool, RintW, which efficiently computes the base-pairing probability distributions over the Hamming distance from arbitrary reference secondary structures. The proposed approach has been demonstrated on ROSE element RNA thermometer sequence and Lysine RNA ribo-switch, showing that the proposed approach captures conformational changes in secondary structures.ConclusionsWe have shown that alternative secondary structures are captured by decomposing base-paring probabilities over Hamming distance. Source code is available from http://www.ncRNA.org/RintW.
Highlights
It is known that functional RNAs often switch their functions by forming different secondary structures
In order to establish the method to decompose the base-pairing probabilities (BPPs) of a whole RNA sequence, we have developed RintW, a new computational tool that efficiently compute the exact base-pairing probability distribution over the Hamming distance from the reference structure
The Boltzmann distribution, often has multiple clusters of the concentration. Such concentrations may reflect of the essential alternative structures associated to switching functions, which are observed in several functional RNAs such as ribo-switches and thermometers
Summary
It is known that functional RNAs often switch their functions by forming different secondary structures. Results: We proposed a new computational method to detect essential alternative secondary structures from RNA sequences by decomposing the base-pairing probability matrix. The decomposition is calculated by a newly implemented software tool, RintW, which efficiently computes the base-pairing probability distributions over the Hamming distance from arbitrary reference secondary structures. Several functional RNAs, such as RNA thermometers and ribo-switches, change their functions by forming different secondary structures. It is difficult, to detect such structural changes. There are bioinformatics tools to predict suboptimal structures [7], but it is difficult to detect which alternative secondary structures are essential
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