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

ABSTRACT:

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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.

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URL http://www.plantbio.uga.edu/~russell/index.php?s=1&n=5&r=0.

SUBMITTER: Manzourolajdad A

PROVIDER: S-EPMC3538908 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature

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

Manzourolajdad Amirhossein A Wang Yingfeng Y Shaw Timothy I TI Malmberg Russell L RL

Journal of theoretical biology 20121114

<h4>Unlabelled</h4>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. Sur ...[more]

PMID: 23160142

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Dataset Information

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

Unlabelled

Availability

Publications

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

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