Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA

JOURNAL OF THEORETICAL BIOLOGY

卷:318

Article

Manzourolajdad, Amirhossein¹  Wang, Yingfeng²  Shaw, Timothy I.¹  Malmberg, Russell L.^1,3 

[1] Univ Georgia, Inst Bioinformat, Athens, GA 30602 USA

[2] Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA

[3] Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA

关键词: RNA secondary structure;    Stochastic context-free grammars;    Structural entropy;    Riboswitch;    Structural ambiguity;   

DOI  :  10.1016/j.jtbi.2012.10.023

来源: Elsevier

【 摘 要 】

RNA secondary structure ensembles define probability distributions for alternative equilibrium secondary structures of an RNA sequence. Shannon's entropy is a measure for the amount of diversity present in any ensemble. In this work, Shannon's entropy of the SCFG ensemble on an RNA sequence is derived and implemented in polynomial time for both structurally ambiguous and unambiguous grammars. Micro RNA sequences generally have low folding entropy, as previously discovered. Surprisingly, signs of significantly high folding entropy were observed in certain ncRNA families. More effective models coupled with targeted randomization tests can lead to a better insight into folding features of these families. Availability: URL . (C) 2012 Elsevier Ltd. All rights reserved.

【 授权许可】

Free