Example of design and filter methods applied by NEXT-RNAi. (a) Visualization of the Paf-AHalpha gene model and transcripts. Regions labeled as 'common region' serve as input for NEXT-RNAi (ORF = open reading frame, UTR = untranslated region). (b) Quality measures computed by NEXT-RNAi for the common regions. Blue and red regions label predicted low-complexity regions (including CAN repeats) and 19-nucleotide off-target regions, respectively. The lower panel shows the predicted siRNA efficiency according to Shah et al.  (averaged for ten siRNAs). (c) NEXT-RNAi predictions of optimal target sites (green) after discarding 19-nucleotide off-target and low complexity regions and regions <150 nucleotides or >250 nucleotides. If available, these regions are directly used as templates for primer designs (left and middle panels). Otherwise, a redesign method is used that connects closest 'optimal' neighbors until a region suitable for primer designs is identified (right panel). Potential dsRNAs are finally ranked by their specificity and efficiency.
Horn et al. Genome Biology 2010 11:R61 doi:10.1186/gb-2010-11-6-r61