TY - JOUR
T1 - Efficient calculation of exact probability distributions of integer features on RNA secondary structures
AU - Mori, Ryota
AU - Hamada, Michiaki
AU - Asai, Kiyoshi
N1 - Publisher Copyright:
© 2014 Mori et al.
Copyright:
Copyright 2017 Elsevier B.V., All rights reserved.
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
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U2 - 10.1186/1471-2164-15-S10-S6
DO - 10.1186/1471-2164-15-S10-S6
M3 - Article
C2 - 25560710
AN - SCOPUS:84964313721
VL - 15
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
M1 - S6
ER -