Additional information

This web server is based on two core applications:

RNAfbinv

RNAfbinv (RNA fragment base inverse) was developed in Danny Barash's lab, see article: L. Weinbrand, A. Avihoo, D. Barash. RNAfbinv: An Interactive Java Application for Fragment-Based Design of RNA Sequences. Bioinformatics, 29(22) , 2938-2940 (2013).
The tool uses a simulated annealing process to design sequences that fold as the target structure and/or its coarse grained tree-graph shape. RNAfbinv is focused on fragment based design, to allow the user a greater flexibility in the design.
RNAfbinv download link: RNAfbinv webpage

incaRNAtion

IncaRNAtion was developed in collaboration between Jérôme Waldispühl's lab and Yann Ponty, see article: V. Reinharz, Y. Ponty and J. Waldispühl: A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distribution Bioinformatics 29 (13), i308-i315 (2013) The tool samples stochastically from the whole sequence space weighting in favour of sequences with high affinity with the target structure in linear time. IncaRNAtion allows the control of the GC content and sequence constraints without biasing the sampling.
incaRNAtion download link: incaRNAtion webpage

Implementation

The web server runs on Tomcat 8. The backend is implemented using Java EE. The frontend generates JSP web pages.
It is designed using the bootstrap css framework and utilizes JavaScript, JQuery, JSON and ajax.

Citation

M. Drory Retwitzer, V. Reinharz, Y. Ponty, J. Waldispühl, D. Barash
IncaRNAfbinv: a web server for fragment-based design of RNA sequences
Nucleic Acids Research 2016
doi: 10.1093/nar/gkw440

About us

The web server was developed by Matan Drory et al. in Dr. Danny Barash's lab at Ben-Gurion University, Beer Sheva, Israel. For all relevant issues and suggestions please contact Matan Drory: matandro@cs.bgu.ac.il