siRNA Selection Server: an automated siRNA oligonucleotide prediction server
Whitehead Institute for Biomedical Research, Bioinformatics and Research Computing, Nine Cambridge Center, Cambridge, MA 02142, USA, 1 Max Planck Institute for Biophysical Chemistry, Göttingen, Germany and 2 Laboratory of RNA Molecular Biology, Rockefeller University, NY 10021, USA
* To whom correspondence should be addressed. Tel: +1 617 258 5000; Fax: +1 617 258 5578; Email: sirna-help{at}wi.mit.edu
Received February 15, 2004; Revised and Accepted March 5, 2004
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.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.
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