To improve the accuracy of targets in RNAi based assays, use our RNAi on- and off-target prediction against standard human/animal genomes or against the specific genome of your organism under perturbation.
RNA molecule based binding affinity prediction
RNAi perturbation is a powerful tool to discover genes and pathways involved in regulation of cellular function. Potent siRNAs are developed using bioinformatics approaches so that they target a unique site in a specific gene. However due to differences in the genome of different cell lines, binding sites are not guaranteed to exist and be unique. And due to the nature of RNA binding, siRNAs are likely to bind with a reduced affinity in unspecific positions accross the genome. Off-target effects are related to the siRNA and often arise from partial complementarily of the sense or antisense strands to an unintended target.
Phenotypic effects observed in the experiment are a superposition of a number of perturbations taking place simultaneously. To avoid false positive leads, RNAi on- and off-target analysis helps to get the most up-to-date target predictions on the organism or cell line in use.
To uncover the set of potential binding sites, we apply on- and off-target-mapping using bioinformatics tools. Mapping against the specific genome of the cell line under observation ensures accurate leads. The number of off-targets and their binding energy are possible indicators to curate hit lists of noisy candidates.