Overview: 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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Research Tools
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siDirect (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.
http://design.rnai.jp/
Added: Fri Mar 23 2007, Hits: 766, Reviews: 0 Write review Cached - 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.
http://jura.wi.mit.edu/bioc/siRNAext/
Added: Fri Jun 20 2003, Hits: 3132, Reviews: 0 Write review Cached -
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.
https://rnaidesigner.invitrogen.com/sirna/
Added: Thu May 20 2004, Hits: 2083, Reviews: 0 Write review -
RNAi Design
(IDT)
Free online RNAi design with flash tutorial.
http://www.idtdna.com/Scitools/Applications/RNAi/R...
Added: Wed Mar 24 2004, Hits: 3175, Reviews: 0 Write review Cached -
RNAi Explorer
(Gene Link)
Custom siRNA search and design. Featuring Gene Link’s proprietary algorithms to design siRNA’s bound to silence the gene.
http://www.genelink.com/sirna/RNAicustomorder.asp
Added: Fri Mar 23 2007, Hits: 373, Reviews: 0 Write review Cached -
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.
http://sfold.wadsworth.org/sirna.pl
Added: Fri Jun 20 2003, Hits: 2053, Reviews: 0 Write review Cached -
siRNA Design Software
(Vivien Kwan, The University of Hong Kong)
SDS (siRNA Design Software) is a software tool that helps to design siRNAs for silencing gene expression. The tool takes an mRNA sequence and makes use of existing design tools to output a set of candidates. These candidates are then filtered based on the secondary structure.
http://i.cs.hku.hk/~sirna/software/sirna.php
Added: Fri Mar 23 2007, Hits: 494, Reviews: 0 Write review Cached -
siRNA Target Finder
(Ambion)
This tool follows the siRNA design guidelines first described by Tuschl and colleagues. In general, Ambion finds that ~50% of siRNAs designed using this tool will reduce target gene expression by>50%.
http://www.ambion.com/techlib/misc/siRNA_finder.ht...
Added: Fri Mar 23 2007, Hits: 457, Reviews: 0 Write review Cached -
siRNA Target Finder
(GenScipt)
A software tool to identify unique candidate siRNA target sequence in your cDNA sequence.
https://www.genscript.com/ssl-bin/app/rnai
Added: Fri Mar 23 2007, Hits: 394, Reviews: 0 Write review -
siSearch
(Stockholm Bioinformatics Center)
siSearch is designed to select siRNAs based on approaches derived from data mining of our siRNA database. We also allow common methods of siRNA design to be included in the search. This includes motif rules, energy conditions and specificity searching. In most cases the default parameters will be sufficient.
http://sonnhammer.cgb.ki.se/siSearch/siSearch_1.7....
Added: Fri Mar 23 2007, Hits: 386, Reviews: 0 Write review Cached