TGS Algorithm
The TGS algorithm is used to predict sites susceptible to RNA directed transcriptional silencing.
This algorithm allows the user to enter any genomic locus, promoter, exon, 5' UTR, etc, and will select small RNA target sites that work to epigenetically remodel the desired target locus.
The algorithm has been found to have a success rate of ~58% and the region being targeted needs to be trancriptionally active.
Developed by the Morris lab, this algorithm allows for promoter sequences (~200-800bp) to be input (in arial font) and the top 5 target loci determined. The algorithm attempts to determine target sites as 21mers but may default to the seed sequence. Thus, the top candidates need to be taken and assessed, relative to the promoter target, or expanded/shortened input and re-assessed. The key is to retain particular purine strings from bp 4-12 in the target. The target sequences, produced by the algorithm are then to be generated as small antisense RNAs, antisense to the algorithm deterimined target, and tested for their ability to direct transcriptional gene silencing.
Here is a video representation of Transcriptional Gene Silencing.
*note this is algorithm is freely available to academics. Industrial related entities need to contact the Technology Transfer office at The Scripps Research Institute (Phone: (858) 784-8140)).
Contact the lab with questions regarding the TGS Algorithm.