Dataset Information
Efficient calculation of exact probability distributions of integer features on RNA secondary structures.
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ABSTRACT: Background
Although the needs for analyses of secondary structures of RNAs are increasing, prediction of the secondary structures of RNAs are not always reliable. Because an RNA may have a complicated energy landscape, comprehensive representations of the whole ensemble of the secondary structures, such as the probability distributions of various features of RNA secondary structures are required.Results
A general method to efficiently compute the distribution of any integer scalar/vector function on the secondary structure is proposed. We also show two concrete algorithms, for Hamming distance from a reference structure and for 5'-3' distance, which can be constructed by following our general method. These practical applications of this method show the effectiveness of the proposed method.Conclusions
The proposed method provides a clear and comprehensive procedure to construct algorithms for distributions of various integer features. In addition, distributions of integer vectors, that is a combination of different integer scores, can be also described by applying our 2D expanding technique.
SUBMITTER: Mori R
PROVIDER: S-EPMC4304215 | biostudies-literature | 2014
REPOSITORIES: biostudies-literature
Publications
Efficient calculation of exact probability distributions of integer features on RNA secondary structures.
BMC genomics 20141212
<h4>Background</h4>Although the needs for analyses of secondary structures of RNAs are increasing, prediction of the secondary structures of RNAs are not always reliable. Because an RNA may have a complicated energy landscape, comprehensive representations of the whole ensemble of the secondary structures, such as the probability distributions of various features of RNA secondary structures are required.<h4>Results</h4>A general method to efficiently compute the distribution of any integer scala ...[more]