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

Matan Drory Retwitzer, Vladimir Reinharz, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, Danny Barash

Research output: Contribution to journalArticlepeer-review

Abstract

RNA design has conceptually evolved from the inverse RNA folding problem. In the classical inverse RNA problem, the user inputs an RNA secondary structure and receives an output RNA sequence that folds into it. Although 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 non-coding RNA 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. incaRNAfbinv 2.0 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.

Original languageEnglish
Pages (from-to)2920-2922
Number of pages3
JournalBioinformatics
Volume36
Issue number9
DOIs
StatePublished - 1 May 2020

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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