RNAi target sequence prediction

This tool predicts RNAi target sites within a nucleotide sequence. The rules used for target site prediciton are a combined set taken from the following papers :

Khvorova A, Reynolds A and Jayasena SD. Functional siRNAs and miRNAs Exhibit Strand Bias. Cell. 2003. Vol. 115:209-216.
Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell. 2003. Vol.115:119-208.

At present the scoring system is very simple. To begin with, all 21 mers ending with a 'C' are found and given a default score of 1. Potential target sequences are discarded if they contain a contiguous set of 4+ A/T's or 3+ C/G's. A single point is added to the score of a potential target sequence for each of the following attributes:

  1. AA at the start of the sequence
  2. G at the start of the sequence (AAG is a special case that scores for both items 1 and 2)
  3. AT rich in the region from bp 9 - 14 (sense strand)
  4. 9-14 bp region contains a C that may be replaced with a U (for mismatch/wobble base pair)
  5. Overall GC content of 30 -> 50%

(FASTA format)
Score threshold