RiDDLE
RNAi by DEQOR-designed lookup of esiRNAs
Idea: web-based database of DEQOR-optimized esiRNAs for human, mouse and rat.
DEQOR-optimization of esiRNAs in HT
We have used a stand-alone version of DEQOR to select the optimal region within a transcript for producing an efficient esiRNA. Each gene is represented, if possible, by a single esiRNA.
Identifying Longest Common Substrings (LCS) using Suffix Arrays
To find the longest common stretch between several transcript variants, we have used a modified version of an algorithm called 'Suffix Arrays'.
The Genome-wide Pipeline
Find the pipeline of the genome-wide esiRNA design process below.
The RiDDLE Database
The RiDDLE database holds esiRNA information for each gene for the three species human, mouse and rat. The entries are fully annotated and orthologues are linked via the HomoloGene database. Users can search for individual genes, domain families, functional annotations, as well as orthologous genes.
Click here to go to the MPI-CBG RiDDLE database