What is RNAi?
RNAi Animations and Tutorials
RNAi Protocols
RNAi Databases
- HuSiDa: Human siRNA Database
- RNAiDB: C. elegans RNAi Database
- RNAi Database of human and mouse shRNA clones: At National RNAi Core Facility, Institute of Molecular
Biology, Academia Sinica, Taiwan
- Database of siRNA sequences of human, mouse, rat, etc.
- Lentiweb siRNA Database
- RNAi Codex: A database that curates publicly available RNAi resources
- siRecords: A collection of mammalian siRNA records (Ren Y, Gong W, Xu Q, Zheng X, Lin D, Wang Y, Li T: siRecords: an extensive database of mammalian siRNAs with efficacy ratings. Bioinformatics 2006, 22:1027-1028.)
- GenomeRNAi: A database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells (Ref: Thomas Horn, Zeynep Arziman, Juerg Berger, and Michael Boutros, Nucleic Acids Res., January 2007; 35: D492 - D497)
- Drosophila RNAi Screening Center
at Harvard Medical School
- Tarbase: A database of animal microRNA targets (Ref: Sethupathy, P., Corda, B., and Hatziegeorgiou, A.G. 2006. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 12:192-197)
- siRNA Database
- siRNA Probe Database (NCBI)
- miRBase: An miRNA database
- ARGONAUTE: A database for gene regulation by mammalian micro-RNAs
- miRGen: Ref: miRGen: a database for the study of animal microRNA genomic organization and function, Nucleic Acids Res. 2006
- miRNA Precursor Candidates for Arabidopsis thaliana
RNAi Bioinformatics
- Computational modeling of RNAi
- Tips For Designing Your Own siRNAs
- siRNA Design Guidelines (Ambion)
- siSearch: An siRNA design program
- BLOCK-iT RNAi Designer: A software from Invitrogen
- siRNA Selection Program: From Whitehead Institute for Biomedical Research
- siRNA Target Finder: A software from Ambion
- E-RNAi: De-novo design of long dsRNAs Nucleic Acids Res. 2005 July 1; 33(Web Server issue): W582–W588
- iRNAi: RNAi oligo designing software
- Deqor: Design and quality control of RNAi (Ref: Henschel, A., Buchholz, F., Habermann, B., NAR 32,W113-W120 (2004): DEQOR, a web-based tool for the Design and Quality Control of siRNAs)
- Jack Lin's siRNA sequence finder
- siRNA Target Finder: From GenScript
- siRNA Construct Builder: A software tool to build small hairpin insert from siRNA target for expression vector
- siDirect : (Ref: siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference Nucleic Acids Research 2004, 32:W124-W129)
- siVirus: Efficient antiviral siRNA design (Ref: Yuki Naito, Kumiko Ui-Tei, Toru Nishikawa, Yutaka Takebe and Kaoru Saigo. (2006)
siVirus: web-based antiviral siRNA design software for highly divergent viral sequences.
Nucleic Acids Res., 34, W448-W450)
- MiRscan: microRNA gene prediction
- RNAmicro: Recognizing miRNA Precursors in Comparative Genomics Data
- miRanda: microRNA Target Detection
- miRacle: miRNA target prediction based on RNA secondary structure (Institute of Genomics and Integrative Biology; Ref: Vinod Scaria,Manoj hariharan, Shiva Kumar , Souvik Maiti and Samir Kumar Brahmachari
miRacle: Server for microRNA Target Prediction incorporating RNA Secondary Structure)
- EuMir: Eukaryotic microRNA precursor prediction server (Institute of Genomics and Integrative Biology)
- MAMI: Meta-prediction of human microRNA targets
- microInspector: A scanning software for detection of miRNA binding sites
- miRTar: A tool to identify miRNA targets against the 3'-UTR of mRNA of mammalian genes
- RNA22 microRNA target detection (Ref: A pattern-based method for the identification of microRNA-target sites and their corresponding RNA/RNA complexes T. Huynh, K. Miranda, Y. Tay, Y.-S. Ang, W.-L. Tam, A. M. Thomson, B. Lim, I. Rigoutsos Cell, Vol 126, 1203-1217, 22 September 2006)
- miRU: Plant microRNA Potential Target Finder
- miRbase Target Database (A database of miR targets on 3' UTR of genes)
- ProMiR: Probabilistic miRNA prediction
- PicTar: An algorithm for the identification of microRNA targets
- TargetScan: Search for predicted microRNA targets
- DIANA MicroTest
- RNAhybrid: microRNA target prediction
- siRNA Hairpin Oligonucleotide Sequence Designer
- shRNA design tool
- HairpinFetcher: An algorithm for finding hairpin forming potential of nucleotide sequences (Institute of Genomics and Integrative Biology)
- EnergyCalculator: An siRNA analysis tool
- TROD (T7 RNAi Oligo Designer)
- siRNA Design Tool (Qiagen)
- SpecificityServer: A tool for checking the specificity of a given siRNA
RNAi and Medicine
A few review articles on RNAi
