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