NEXT-RNAi is a software for the design and evaluation of genome-wide RNAi libraries and performs all steps from the prediction of specific and efficient RNAi target sites to the visualization of designed reagents in their genomic context. The software enables the design and evaluation of siRNAs and long dsRNAs and was implemented in an organism-independent manner allowing designs for all sequenced and annotated genomes. It requires the minimal input of desired target sequences and an off-target database.
NEXT-RNAi implements several methods to predict a reagents' quality and offers many special features such as the straight-forward design of independent RNAi reagents. How these quality parameters are assessed and an overview about NEXT-RNAi features is available here.
NEXT-RNAi can be incorporated into Galaxy to create re-usable workflows and use Galaxy as web-front end. Here is a how-to guide.
Please contact us for questions or suggestions:
Thomas Horn, Thomas Sandmann and Michael Boutros. Design and evaluation of genome-wide libraries for RNAi screens. Genome Biol. 2010 Jun 15;11(6):R61. [Link to manuscript]