Abstract
We present new modifications to the Wuchty algorithm in order to better define and explore possible conformations for an RNA sequence. The new features, including parallelization, energy-independent lonely pair constraints, context-dependent chemical probing constraints, helix filters, and optional multibranch loops, provide useful tools for exploring the landscape of RNA folding. Chemical probing alone may not necessarily define a single unique structure. The helix filters and optional multibranch loops are global constraints on RNA structure that are an especially useful tool for generating models of encapsidated viral RNA for which cryoelectron microscopy or crystallography data may be available. The computations generate a combinatorially complete set of structures near a free energy minimum and thus provide data on the density and diversity of structures near the bottom of a folding funnel for an RNA sequence. The conformational landscapes for some RNA sequences may resemble a low, wide basin rather than a steep funnel that converges to a single structure.
Highlights
The flood of RNA sequence information from new high-throughput technologies creates a need for efficient computational tools for predicting structure and function
The parallelization of the Wuchty code proceeded with the original Vienna group implementation of the Wuchty algorithm [15,16]
This paper presents new modifications to include experimental constraints in the Wuchty algorithm that facilitate defining the possible secondary structures for an RNA sequence
Summary
The flood of RNA sequence information from new high-throughput technologies creates a need for efficient computational tools for predicting structure and function. Predicting an RNA secondary structure is often the first step towards discovering the structure and function of a new noncoding RNA sequence. Free energy minimization is the most common approach to generate an RNA structure prediction [1,2]. The thermodynamic parameters that form the basis of most free energy minimization algorithms are constantly being updated and improved [3,4]. Free energy minimization does not consider RNA tertiary interactions, RNAprotein interactions, kinetic traps, or cotranscriptional folding [5]. For long RNA sequences, PLOS ONE | DOI:10.1371/journal.pone.0117217. For long RNA sequences, PLOS ONE | DOI:10.1371/journal.pone.0117217 February 19, 2015
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