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.
- SiRNA at Whitehead (Whitehead Institute for Biomedical Research)
This online tool helps you select oligos to knock down your gene of interest. After entering your sequence, choosing a pattern for your oligo nucleotides, and selecting various filter methods, you will be presented with a list of oligos matching your pattern. From this list, select those oligos you would like to consider further, based on their position within your sequence, the snps, and other criteria. Your results will be available directly on the web and/or will be emailed to you when they are ready. Needs registration which is free.
Added: Fri Jun 20 2003, Hits: 4416, Reviews: 0
(Yuki Naito et al. University of Tokyo)
A web-based online software system for computing highly effective small interfering RNA (siRNA) sequences with maximum target-specificity for mammalian RNA interference (RNAi). It also provides off-target search.
Added: Wed Feb 04 2009, Hits: 909, Reviews: 0
AsiDesigner: exon-based siRNA design server considering alternative splicing
(Bioinformatics Research Center, KRIBB)
AsiDesigner is a siRNA design program based on exon-based siRNA design algorithm considering alternative splicing.
Added: Mon Aug 20 2012, Hits: 656, Reviews: 0
BLOCK-iT RNAi Designer
Allows you to design synthetic siRNA, Stealth RNA, or shRNA molecules from nucleotide target sequences, or convert an siRNA molecule sequence into a Stealth?molecule or shRNA molecule. It uses its proprietary algorithm or Tuschl's rules for siRNA design, and blasts an internal database for homology check, which is fast and the results are almost instantly displayed.
Added: Thu May 20 2004, Hits: 2586, Reviews: 0
(University of Nebraska-Lincoln)
Picks siRNAs for an input sequence. No BLAST search enforced.
Added: Mon Aug 20 2012, Hits: 707, Reviews: 0
Free online RNAi design with flash tutorial.
Added: Wed Mar 24 2004, Hits: 2780, Reviews: 0
Returns siRNAs for a given gene sequence by Accession number and performs BLAST search for candidate siRNAs.
Added: Mon Aug 20 2012, Hits: 1098, Reviews: 0
Sirna - SiRNA Design
(Wadsworth Bioinformatics Center)
Sfold aims to provide tools for improved siRNA design by combining secondary structure and accessibility prediction with empirical design rules. Free.
Added: Fri Jun 20 2003, Hits: 2180, Reviews: 0