OptiRNAi 2.0                 An RNAi Design Tool

Target selection is the critical step for any RNAi experimentation. OptiRNAi predicts optimum RNAi target sequences using the criteria of  Elbashir et al 2002 and Reynolds et al 2004. The program will generate up to 10 potential siRNA targets with a score indicating how well each matches empirical and theoretical criteria. The updated version has an improved scoring system which focuses on position preference as well as nucleotide composition.

The preferred length of the siRNA target is (the default value is 23)

Load the sequence file

(The sequence can be in either FASTA format or just plain text)

Or paste the sequence here:

(Beginning with the start codon and ending with stop codon is preferred.
Coding regions can be obtained by finding the webpage for your gene
of interest at NCBI and clicking on the CDS link

Publication: Cui et al, OptiRNAi, an RNAi design tool, Comput Methods Programs Biomed. 2004 Jul; 75 (1):67-73.

Wenwu Cui
Laboratory of Receptor Biology and Gene Expression
National Cancer Institute
National Institutes of Health