RNA-MoIP

This web server is based RNA-MoIP, developed in the lab of Jérôme Waldispühl. See article Reinharz, V., Major, F., Waldispühl, J. Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics 28(12): i207-14 (2012).

RNA-MoIP is an integer programming framework that refines predicted secondary structures (i.e. removes incorrect canonical base-pairs) to accommodate the insertion of RNA 3D motifs (i.e. hairpins, internal loops and k-way junctions). The predictions can be used as templates to generate complete 3D structures with the MC-Sym program.

RNA-MoIP download link: RNA-MoIP Webpage

Implementation

The server runs on an Ubuntu-Server on a Dell PE T610 2x Intel Quad core X5570 Xeon Processor, 2.93 GHz 8M Cache, 64 GB Memory (8 x 8 GB), 1333 MHz Dual Ranked RDIMMs for 15 Processors, Advanced ECC. The frontend generates python web pages. It is designed using the bootstrap css framework and utilizes Python, JavaScript, JQuery, ajax and bash.

Citation

  1. Jason Yao, Vladimir Reinharz, François Major and Jérôme Waldispühl. RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W440–W444, https://doi.org/10.1093/nar/gkx429
  2. Jérôme Waldispühl and Vladimir Reinharz. Modeling and predicting rna three-dimensional structures. Methods Mol Biol, 1269:101-21, 2015.
  3. Vladimir Reinharz, François Major, and Jérôme Waldispühl. Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics (Proceedings of ISMB 2012; Also appear in Conference Section), 28(12):i207-14, June 2012.

About Us

The web server was developed by Jason Yao et al. in Dr. Jérôme Waldispühl's lab at McGill University, Montreal, QC. For all relevant issues and suggestions please contact Jérôme Waldispühl: jerome.waldispuhl@mcgill.ca