E-RNAi

RNA interference (RNAi) has become a powerful genetic approach to systematically dissect gene function on a genome-wide scale. Owing to the penetrance and efficiency of RNAi in invertebrates, model organisms such as Drosophila melanogaster and Caenorhabditis elegans have contributed significantly to the identification of novel components of diverse biological pathways, ranging from early development to fat storage and aging. For the correct assessment of phenotypes, a key issue remains the stringent quality control of long double-stranded RNAs (dsRNA) to calculate potential off-target effects that may obscure the phenotypic data. We here describe a web-based tool to evaluate and design optimized dsRNA constructs. Moreover, the application also gives access to published predesigned dsRNAs. The E-RNAi web application is available at http://e-rnai.dkfz.de/.[1]

The design of RNA interference (RNAi) reagents is an essential step for performing loss-of-function studies in many experimental systems. The availability of sequenced and annotated genomes greatly facilitates RNAi experiments in an increasing number of organisms that were previously not genetically tractable. The E-RNAi web-service, accessible at http://www.e-rnai.org/, provides a computational resource for the optimized design and evaluation of RNAi reagents. The 2010 update of E-RNAi now covers 12 genomes, including Drosophila, Caenorhabditis elegans, human, emerging model organisms such as Schmidtea mediterranea and Acyrthosiphon pisum, as well as the medically relevant vectors Anopheles gambiae and Aedes aegypti. The web service calculates RNAi reagents based on the input of target sequences, sequence identifiers or by visual selection of target regions through a genome browser interface. It identifies optimized RNAi target-sites by ranking sequences according to their predicted specificity, efficiency and complexity. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design. Results are presented online, as a downloadable HTML report and as tab-delimited files.[2]

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