The design of RNA interference (RNAi) reagents is an essential step for performing loss-of-function studies in many experimental systems. The availability of sequenced and annotated genomes greatly facilitates RNAi experiments in an increasing number of organisms that were previously not genetically tractable.
Allows users to generate siRNAs for mammalian RNA interference (RNAi). siDirect starts from an accession number or a nucleotide sequence and provides effective siRNA candidates with various information such as a graphical view, a downloadable list and related information. The application includes multiple options to customize the submission including the possibility of minimization of seed-dependent off-targets effects or the ability to avoid contiguous A’s or T’s cells.
A web-app for the design of Stealth RNAi™ siRNA. For three best Stealth RNAi™ siRNA sequences designed by the BLOCK-iT™ RNAi Designer, two of them give greater than 70% knockdown of mRNA, given that the transfection efficiency in your experiment is at least 80%. If two or more fail to knock down your target RNA by at least 70% under these conditions, BLOCK-iT RNAi Designer will design and ship a fourth Stealth RNAi™ siRNA to your target for free.
Offers a platform dedicated to reagents management. E-RNAi contains two mains functions: (i) allowing users to select target sequences for creating reagents and; (ii) assessing existing RNAi reagents. The application can deal with long dsRNAs, siRNAs and includes twelve implemented genomes such as Acyrthosiphon pisum, Apis mellifera or Aedes aegypti. Nevertheless, these organisms can be extended by user request.
Automates artificial microRNAs (amiRNAs) design. WMD3 uses the favorite gene(s), which the user want to silence, and designs 21mer amiRNA sequences. User will retrieve oligo sequences to express the small RNA from endogenous miRNA precursors. WMD3 was initially implemented for Arabidopsis thaliana, but has now been extended to more than 30 additional species for which genome or extensive EST (expressed sequence tag) information is available. WMD3 is designed to optimize both intrinsic small RNA properties as well as specificity within the given transcriptome.
Predicts the probability that an mRNA fragment will cross-react with other genes in the cell and helps researchers to design experiments to test the specificity of esiRNAs or chemically designed siRNAs.