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Online siRNA Design Tools

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  • AsiDesigner 0.00 (Bioinformatics Research Center, KRIBB) - AsiDesigner is a highly performing, highly effective siRNA design program based on exon-based siRNA design algorithm considering alternative splicing.
  • Block-iT RNAi Designer 0.00 (Invitrogen) - Design custom RNA molecules for all RNAi applications. You can design synthetic siRNA, Stealth? RNA, or shRNA molecules from nucleotide target sequences, or you convert an siRNA molecule sequence into a Stealth? molecule or shRNA molecule. You can give a RefSeq accession number or cDNA sequence. The program can blast sequence databases of different organisms to find unique regions on your sequence as targets.
  • Gene specific siRNA selector 0.00 (ioinformatics Facility, The Wistar Institute) - Small interfering RNA (siRNA) is used in functional genomics applications to decrease the expression of a target gene, which may yield a biological effect that suggests a function for the target gene. The siRNA design tool scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules. Selected candidates are then screened to identify those siRNA sequences that are specific to the gene of interest.
  • siDESIGN Center 0.00 (Dharmacon) - Uses rational siRNA design algorithm for RNAi target slection. It also provides local BLAST tool which scans species-specific UniGene databases for homology.
  • SiRNA at Whitehead 0.00 - This online tool helps you select oligos to knock down your gene of interest. After entering your sequence, choosing a pattern for your oligo nucleotides, and selecting various filter methods, you will be presented with a list of oligos matching your pattern. From this list, select those oligos you would like to consider further, based on their position within your sequence, the snps, and other criteria. Your results will be available directly on the web and/or will be emailed to you when they are ready. Needs registration which is free.
  • siRNA Design 0.00 (IDT) - Design siRNA following the rules of either T. Tuschl or A. Fire. Accept accession number or sequence as input. No database blasting.
  • siRNA Target Finder 0.00 (Ambion) - Paste your mRNA sequence into the window, choose your preferred end structure (3' TT or UU), and the program will scan your sequence for AA dinucleotides. A report is generated indicating the position of the AA dinucleotide, the 21 base target and the corresponding sense and antisense siRNA oligonucleotides.
  • siRNA Target Finder 0.00 (GeneScript) - Find siRNA target. Acceptable input are accession number and sequence. Five databases including human, mouse, rat and drosophila are available for blasting.
  • TROD: T7 RNAi Oligo Designer 0.00 (Dudek P and Picard D.) - a web application that facilitates the design of DNA oligonucleotides for the synthesis of short interfering RNAs (siRNAs) with T7 RNA polymerase. It takes a cDNA sequence as input and automatically generates the appropriate DNA oligos for ordering. The output is organized so as to make it easy for the user to choose appropriate target sequences.

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