title: siRNA specificity searching incorporating mismatch tolerance data.
abstract: Artificially synthesized short interfering RNAs (siRNAs) are widely used in functional genomics to knock down specific target genes. One ongoing challenge is to guarantee that the siRNA does not elicit off-target effects. Initial reports suggested that siRNAs were highly sequence-specific; however, subsequent data indicates that this is not necessarily the case. It is still uncertain what level of similarity and other rules are required for an off-target effect to be observed, and scoring schemes have not been developed to look beyond simple measures such as the number of mismatches or the number of consecutive matching bases present. We created design rules for predicting the likelihood of a non-specific effect and present a web server that allows the user to check the specificity of a given siRNA in a flexible manner using a combination of methods. The server finds potential off-target matches in the corresponding RefSeq database and ranks them according to a scoring system based on experimental studies of specificity.
  
  
  BACKGROUND
  The server is available at http://informatics-eskitis.griffith.edu.au/SpecificityServer.
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden.
authors.forename: Alistair M
authors.initials: AM
authors.lastname: Chalk
authors.forename: Erik L L
authors.initials: EL
authors.lastname: Sonnhammer
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D030541:Databases, Genetic; D020868:Gene Silencing; D018390:Gene Targeting / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D034741:RNA, Small Interfering / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D034741:RNA, Small Interfering