**Author details**

274 Bioinformatics

Das et al reported designing of a siRNA designing tool using a simple approach towards minimizing miRNA-like off-target effect through user feedback. Here, the user can actually choose from the list of potential off-target genes, the off-targets he/she wants to filter out, by considering the effect of silencing of those off-target genes. This tool statistically evaluates present day siRNA design rules such as- low GC content, absence of long stretches of identical nucleotides, thermodynamic conditions favouring efficient RISC entry, absence of homology to other mRNAs, absence of immune stimulatory motifs in the RISC entering strand of the siRNA duplex and some position specific nucleotide compositions, in a database of validated siRNAs [12] used in experiments to examine the threshold parameters. A support vector machine, trained with the optimal features set, is used for classifying potential and effective siRNAs. Moreover, with other parameters, it predicts the potential miRNA-like off-target genes for each candidate siRNA, sets a threshold for the number of off-targets to minimize miRNA-like off-target effect and presents the list of predicted off-target genes. A feedback mechanism allows the user to choose specific genes that needs to be filtered out from the list of predicted off-target genes recursively until his/her needs are met. This technique gives a more

As many guidelines are available for selection of efficient siRNAs and they promise to improve efficacy in silencing, much progress has been made in designing siRNAs with improved targeting success rate. Now the main challenge in in-silico siRNA design is reducing the unintended effects arising from inadvertent targets. While the off-targets with near perfect sequence complementarity with the given siRNA is taken care of much efficiently by targeting against a unique region of the target mRNA, which can be found by homology searching with other mRNAs of the organism, miRNA-like off-targets remain to be addressed with efficiency. The few online siRNA designing solutions those consider for reducing such off-targets rely on reducing the number of off-targets. Even then a compromise has to be made between potency and specificity as siRNA sequences that could give higher specificity often comes with lower potency. Now approaching this specificity

rational approach towards handling the miRNA-like off- target issue.

**Figure 1.** An example of off-target filtering by user feedback

**10. Conclusion** 

Suman Ghosal, Shaoli Das and Jayprokas Chakrabarti *Indian Association for the Cultivation of Science, Kolkata, India* 
