Visualizing RNA Secondary Structure Base Pair Probabilities
نویسندگان
چکیده
RNAbow diagrams are a versatile tool for visualizing and comparing ensembles of RNA secondary structures. Previously, RNAbows have proved useful when investigating individual ensembles of folds, performing cluster analysis, and identifying conformational changes caused by single nucleotide polymorphisms [Aalberts and Jannen, RNA, 19, 475–478 (2013)]. This contest submission highlights their usefulness in (1) making visual comparisons of the Minimum Free Energy structure to the full structural ensemble and (2) understanding of the effects of mutations on RNA folding stability.
منابع مشابه
Visualizing RNA base-pairing probabilities with RNAbow diagrams.
There are many effective ways to represent a minimum free energy RNA secondary structure that make it easy to locate its helices and loops. It is a greater challenge to visualize the thermal average probabilities of all folds in a partition function sum; dot plot representations are often puzzling. Therefore, we introduce the RNAbows visualization tool for RNA base pair probabilities. RNAbows r...
متن کاملVisualizing RNA Secondary Structure Base Pair Binding Probabilities using Nested Concave Hulls
The challenge 1 of the BIOVIS 2015 design contest consists in designing an intuitive visual depiction of base pairs binding probabilities for secondary structure of ncRNA. Our representation depicts the potential nucleotide pairs binding using nested concave hulls over the computed MFE ncRNA secondary structure. Thus, it allows to identify regions with a high level of uncertainty in the MFE com...
متن کاملThe equilibrium partition function and base pair binding probabilities for RNA secondary structure.
A novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures. In particular, both the partition function and the probabilities of all base pairs are computed by a recursive scheme of polynomial order N3 in the sequence length N. The temperature dep...
متن کاملImproved RNA secondary structure prediction by maximizing expected pair accuracy.
Free energy minimization has been the most popular method for RNA secondary structure prediction for decades. It is based on a set of empirical free energy change parameters derived from experiments using a nearest-neighbor model. In this study, a program, MaxExpect, that predicts RNA secondary structure by maximizing the expected base-pair accuracy, is reported. This approach was first pioneer...
متن کاملRtools: a web server for various secondary structural analyses on single RNA sequences
The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the ...
متن کامل