title: siRNA Selection Server: an automated siRNA oligonucleotide prediction server.
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.
authors.affiliation: Whitehead Institute for Biomedical Research, Bioinformatics and Research Computing, Nine Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Bingbing
authors.initials: B
authors.lastname: Yuan
authors.forename: Robert
authors.initials: R
authors.lastname: Latek
authors.forename: Markus
authors.initials: M
authors.lastname: Hossbach
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
authors.forename: Fran
authors.initials: F
authors.lastname: Lewitter
mesh_terms: D000465:Algorithms; D000818:Animals; D006801:Humans; D020407:Internet; D051379:Mice; D009841:Oligonucleotides / Q000737:chemistry; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000737:chemistry*; D012984:Software; D014584:User-Computer Interface
chemical_list: D009841:Oligonucleotides; D034741:RNA, Small Interfering