Finding siRNA Off-Target Sites

One of the newer methodologies used in target validation is called RNA interference (RNAi). One type of RNAi approach uses the effects of small interfering RNAs (siRNAs) to silence a gene. Because there are many programs that predict what siRNAs and associated target sites are good candidates for RNAi experiments, Pipeline Pilot is ideal for automating these tasks.

The example above shows a protocol that uses the Find siRNA Target Sites component (a program from EMBOSS called sirna) to create a list of potential siRNA target sites. Within the same pipeline, it runs a sequence similarity search using BLASTn to find all potential locations where a predicted siRNA molecule could bind with an organism's genome, thus identifying unwanted off-target sites (in red) and preferred on-target sites ( in green).