RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences

Abstract

Background: RNAexinv is an interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes. It is an extended inverse RNA folding program with the rationale behind that the generated sequences should not only fold into a desired structure, but they should also exhibit favorable attributes such as thermodynamic stability and mutational robustness. RNAexinv considers not only the secondary structure in order to design sequences, but also the mutational robustness and the minimum free energy. The sequences that are generated may not fully conform with the given RNA secondary structure, but they will strictly conform with the RNA shape of the given secondary structure and thereby take into consideration the recommended values of thermodynamic stability and mutational robustness that are provided.

Results: The output consists of designed sequences that are generated by the proposed method. Selecting a sequence displays the secondary structure drawings of the target and the predicted fold of the sequence, including some basic information about the desired and achieved thermodynamic stability and mutational robustness. RNAexinv can be used successfully without prior experience, simply specifying an initial RNA secondary structure in dot-bracket notation and numerical values for the desired neutrality and minimum free energy. The package runs under LINUX operating system. Secondary structure predictions are performed using the Vienna RNA package.

Conclusions: RNAexinv is a user friendly tool that can be used for RNA sequence design. It is especially useful in cases where a functional stem-loop structure of a natural sequence should be strictly kept in the designed sequences but a distant motif in the rest of the structure may contain one more or less nucleotide at the expense of another, as long as the global shape is preserved. This allows the insertion of physical observables as constraints. RNAexinv is available at http://www.cs.bgu.ac.il/~RNAexinv.

Figure 1

RNAexinv Input Screen. Initial GUI screen for providing the RNA secondary structure, as well as neutrality and minimum free energy values that the user would like to use for sequence design.

Figure 2

List of Designed Sequences. Main GUI screen for listing the designed sequences that are generated by multiple runs of RNAexinv. The scores on the right indicate the tree-edit distance between the predicted secondary structure of the designed sequence and that of the input.

Figure 3

Designed Sequence Data. For each designed sequence, relevant secondary structure and accompanied information is provided along with a graphical drawing for both the given initial structure and the predicted secondary structure of the designed sequence.

Figure 4

Comparison of RNAexinv with RNAinverse for miR-146 Example. Comparison of miR-146 wild-type structure (center) with the predicted structure of a designed sequence by RNAinverse (right) and the predicted structure of a designed sequence by RNAexinv (left). The physical attributes of the designed sequence by RNAexinv are significantly closer to that of the wild-type, while the same RNA shape as in the wild-type is retained.