2009/04/23 by Valerie Hower, Hower, Valerie, Christine Heitsch +2
Biochemistry, Genetics and Molecular Biology · Mathematics · #Biomolecules (q-bio.BM) #Combinatorics (math.CO) #FOS: Biological sciences #FOS: Mathematics #Genomics and Phylogenetic Studies #RNA Research and Splicing #RNA and protein synthesis mechanisms #math.CO #q-bio.BM
paper · pdf · doi:10.48550/arxiv.0904.3700
19 pages, 5 figures
arxiv created 2009/04/23 · openalex publication_date 2009/04/23 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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. Our results indicate that variation of these specific parameters does not have a dramatic effect on the structures predicted by the free energy model. We additionally map a collection of known RNA secondary structures to the RNA polytope.