Top : Research Tools : Online Tools : SiRNA Design
Summary: siRNA design for post-transcriptional gene silencing or RNAi is a pretty straightforward. Although many different algorithms and programs are available for siRNA design, the advantages one may have over another are hard to judge. To design a siRNA, an mRNA or cDNA sequence of the gene of interest is required and can be retrieved from the NCBI database. The RefSeq mRNA sequence for the target gene is preferred because it represents the most reliable mRNA sequence for the gene. Some programs can take a RefSeq ID as a sequence input which usually looks like ‘NM_xxxxxx’. The whole length of an mRNA sequence can be targeted although some researchers prefer targeting only the coding region while excluding UTR regions. Some programs provide homology search for candidate siRNA targets against other mRNA sequences of the genome. A siRNA should not have significant homology with unrelated sequences especially at its 3’ end. If a siRNA design program does not provide the function for homology sequence, a manual BLAST search is mandatory for avoiding off-target effects.
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