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RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecules. [Source: Wikipedia]

UP-TORR

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

RNA interference (RNAi) is a widely adopted tool for loss-of-function studies but RNAi results only have biological relevance if the reagents are appropriately mapped to genes. Several groups have designed and generated RNAi reagent libraries for studies in cells or in vivo for Drosophila and other species. At first glance, matching RNAi reagents to genes appears to be a simple problem, as each reagent is typically designed to target a single gene. In practice, however, the reagent-gene relationship is complex.

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si-shRNA Selector

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Prediction of efficient oligonucleotides for RNA interference presents a serious challenge, especially for the development of genome-wide RNAi libraries which encounter difficulties and limitations due to ambiguities in the results and the requirement for significant computational resources. Here we present a fast and practical algorithm for shRNA design based on the thermodynamic parameters.

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rnaworkbench

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

RNA interference (RNAi) has become an important tool to study and utilize gene silencing by introducing short interfering RNA (siRNA). In order to predict the most efficient siRNAs, a new software tool, RNA Workbench (RNAWB), has been designed and is freely available (after registration) on http://www.rnaworkbench.com. In addition to the standard selection rules, RNAWB includes the possibility of statistical analyses of the applied selection rules (criteria).

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IDT SciTools

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

DNA and RNA oligomers are used in a myriad of diverse biological and biochemical experiments. These oligonucleotides are designed to have unique biophysical, chemical and hybridization properties. We have created an integrated set of bioinformatics tools that predict the properties of native and chemically modified nucleic acids and assist in their design.

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TROD

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

We have developed T7 RNAi Oligo Designer (TROD), a web application for RNA interference studies. TROD greatly facilitates the design of oligodeoxynucleotide sequences for the in vitro production of siRNA duplexes with T7 RNA polymerase. Given a query cDNA sequence, the program scans for appropriate target sequences based on the constraints of the T7 RNA polymerase method and published criteria for RNA interference with siRNAs.

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OfftargetFinder

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

RNA interference (RNAi) technology is being developed as a weapon for pest insect control. To maximize the specificity that such an approach affords we have developed a bioinformatic web tool that searches the ever-growing arthropod transcriptome databases so that pest-specific RNAi sequences can be identified. This will help technology developers finesse the design of RNAi sequences and suggests which non-target species should be assessed in the risk assessment process.

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iBeetle-Base

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The iBeetle-Base (http://ibeetle-base.uni-goettingen.de) makes available annotations of RNAi phenotypes, which were gathered in a large scale RNAi screen in the red flour beetle Tribolium castaneum (iBeetle screen). In addition, it provides access to sequence information and links for all Tribolium castaneum genes.

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ATARiS

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Genome-scale RNAi libraries enable the systematic interrogation of gene function. However, the interpretation of RNAi screens is complicated by the observation that RNAi reagents designed to suppress the mRNA transcripts of the same gene often produce a spectrum of phenotypic outcomes due to differential on-target gene suppression or perturbation of off-target transcripts.

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