Parametric Analysis of RNA Branching Configurations
نویسندگان
چکیده
منابع مشابه
Parametric analysis of RNA branching configurations.
Motivated by recent work in parametric sequence alignment, we study the parameter space for scoring RNA folds and construct an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common branching. We use this polytope and its normal fan to study the effect of varying three parameters in the free energy model that are not determined experimentally. Our results in...
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We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common branching. We use this polytope and its normal fan to study the effect of varying three parameters in the free energy model that are not determined experimentally....
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The prevalent method for RNA secondary structure prediction for a single sequence is free energy minimization based on the nearest neighbor thermodynamic model (NNTM). One of the least well-developed parts of the model is the energy function assigned to the multibranch loops. Parametric analysis can be performed to elucidate the dependance of the prediction on the branching parameters used in t...
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ژورنال
عنوان ژورنال: Bulletin of Mathematical Biology
سال: 2011
ISSN: 0092-8240,1522-9602
DOI: 10.1007/s11538-010-9607-3