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. 2004 Jul 1;32(Web Server issue):W130-4.
doi: 10.1093/nar/gkh366.

siRNA Selection Server: an automated siRNA oligonucleotide prediction server

Bingbing Yuan  1 , Robert Latek, Markus Hossbach, Thomas Tuschl, Fran Lewitter
Affiliations

siRNA Selection Server: an automated siRNA oligonucleotide prediction server

Bingbing Yuan et al. Nucleic Acids Res. .

Abstract

The Whitehead siRNA (short interfering RNA) Selection Web Server (http://jura.wi.mit.edu/bioc/siRNA) automates the design of short oligonucleotides that can specifically 'knock down' expression of target genes. These short sequences are about 21 nt in length, and when synthesized as double stranded RNA and introduced into cell culture, can reduce or eliminate the function of the target gene. Depending on the length of a gene, there are potentially numerous combinations of possible 21mers. Some experimental evidence has already shown that not all 21mers in a gene have the same effectiveness at silencing gene function. Our tool incorporates published design rules and presents the scientist with information about uniqueness of the 21mers within the genome, thermodynamic stability of the double stranded RNA duplex, GC content, presence of SNPs and other features that may contribute to the effectiveness of a siRNA.

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Figures

Figure 1
Figure 1
Data input web page to begin design of siRNAs for your target sequence.
Figure 2
Figure 2
This form allows you to select candidate oligos for further analysis.
Figure 3
Figure 3
Result page after a BLAST search is done on candidate oligos.
Figure 4
Figure 4
Summary BLAST results for each candidate siRNA.
See this image and copyright information in PMC

References

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