incaRNAfbinv / RNAfbinv 2.0 – Fragment-based design of RNA sequences

incaRNAfbinv / RNAfbinv 2.0


incaRNAfbinv is a web server which implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs.


RNAfbinv is a fragment based RNA design tool. It uses a simulated annealing process to optimize a 2D RNA structure.


incaRNAfbinv team


  • Linux
  • Python





Retwitzer MD, Reinharz V, Churkin A, Ponty Y, WaldispĆ¼hl J, Barash D.
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs.
Bioinformatics. 2020 May 1;36(9):2920-2922. doi: 10.1093/bioinformatics/btaa039. PMID: 31971575.

incaRNAfbinv: a web server for the fragment-based design of RNA sequences.
Drory Retwitzer M, Reinharz V, Ponty Y, WaldispĆ¼hl J, Barash D.
Nucleic Acids Res. 2016 Jul 8;44(W1):W308-14. doi: 10.1093/nar/gkw440. Epub 2016 May 16.

Bioinformatics. 2013 Nov 15;29(22):2938-40. doi: 10.1093/bioinformatics/btt494. Epub 2013 Aug 23.
RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.
Weinbrand L1, Avihoo A, Barash D.

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