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IncaRNAfbinv 2.0 - A webserver and software with motif control for fragment-based design of RNAs

Abstract : RNA design has conceptually evolved from the inverse RNA folding problem. In the classical inverse RNA problem (Hofacker et al, 1994), the user inputs an RNA secondary structure and receives an output RNA sequence that folds into it. While modern RNA design methods are based on the same principle, a finer control over the resulting sequences is sought. As an important example, a substantial number of ncRNA families show high preservation in specific regions while being more flexible in others and this information should be utilized in the design. By using the additional information, RNA design tools can help solve problems of practical interest in the growing fields of synthetic biology and nanotechnology. IncaRNAfbinv2.0 utilizes a fragment-based approach, enabling a control of specific RNA secondary structure motifs. The new version allows significantly more control over the general RNA shape, and also allows to express specific restrictions over each motif separately, in addition to other advanced features. Availability:incaRNAfbinv2.0 is available through a standalone package and a web-server at https://www.cs.bgu.ac.il/incaRNAfbinv Source code, command-line and GUI wrappers can be found at https://github.com/matandro/RNAsfbinv
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https://hal.inria.fr/hal-02423237
Contributor : Yann Ponty <>
Submitted on : Monday, December 23, 2019 - 5:50:44 PM
Last modification on : Thursday, June 18, 2020 - 12:32:06 PM

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  • HAL Id : hal-02423237, version 1

Citation

Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, et al.. IncaRNAfbinv 2.0 - A webserver and software with motif control for fragment-based design of RNAs. Bioinformatics, Oxford University Press (OUP), In press. ⟨hal-02423237⟩

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