| | | |  | | | | | | | | | | | | | | | |  | | | | :: | | | :: | | | :: | | | :: | | | :: | | | :: | | | :: | | | :: | | | :: | | | :: | | | | | | | | | | | | | | | | | Online siRNA Design Tools Sponsored Links
- siDESIGN Center
 
(Dharmacon, Inc.)
- Uses rational siRNA design algorithm for RNAi target slection. It also provides local BLAST tool which scans species-specific UniGene databases for homology. (Rate:
6 Votes
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) - AsiDesigner - AsiDesigner is a highly performing, highly effective siRNA design program based on exon-based siRNA design algorithm considering alternative splicing. (Rate:
0 Votes
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) - BIOPREDsi - BIOPREDsi is an artificial intelligence algorithm that computationally predicts 21-nt siRNA sequences that have an optimal knockdown effect for a given gene. BIOPREDsi implements a neuronal network, based on the SNNSİ software package, and has been trained using 2,500 randomly selected siRNAs to predict the most potent inhibitory sequences from a set of predicted target-specific siRNAs. Specificity criteria were defined by systematic analysis of a set of 200 mutated siRNAs tested in a reporter gene assay. Each siRNA sequence is designed for specificity within a defined transcriptome and will have generally non-terminal mismatches against any non-targeted transcript.
BIOPREDsi can be used either by uploading a particular sequence or an identifier for a given gene. The software then will design a user-specified number of siRNA sequences that are predicted to have an optimal knockdown effect on the target gene. For every siRNA sequence a score is returned, which reflects the predicted potential of the siRNA to decrease the expression levels of a target mRNA. (Rate:
0 Votes
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)
- SDIR:Design of siRNA - DSIR predicts the gene silencing efficacy of siRNA and suggests candidate siRNA to target a gene according to the predicted efficacy. (Rate:
0 Votes
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- siDRM - siDRM is an implementation of the DRM rule sets for selecting effective siRNAs. These rule sets were obtained in the following three steps: (1) A survey of significant features was conducted on the large and diverse dataset compiled from siRecords, with all known features implicated to have impacts on the siRNA efficacy. This survey resulted in a list of features associated with a significant up-shift of the siRNA efficacy distribution, and/or significantly boosting the chances of achieving higher siRNA efficacy. (2) A feature combination analysis was performed to exploit the positive cooperativity of the significant features identified in their joint effects in boosting the siRNA efficacy. A list of feature combinations (also called rules) leading to substantial improvement in efficacy in the training dataset was obtained. (3) The DRM (or disjunctive rule merging) algorithm was applied to merge and reorganize the rules obtained, resulting in a bundle of rule sets (or disjunctions of rules), ordered descendingly in stringency. (Rate:
0 Votes
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- siRNA Target Finder
(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. (Rate:
2 Votes
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) - Block-iT RNAi Designer
(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. (Rate:
1 Votes
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) - DEQOR
(Henschel et al.)
- a web-based tool for the design and quality control of siRNAs (Rate:
1 Votes
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) - Gene specific siRNA selector
(Bioinformatics 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. (Rate:
0 Votes
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- siDirect
(Naito et al.)
- a web-based online software system for computing highly effective small interfering RNA (siRNA) sequences with maximum target-specificity for mammalian RNA interference (RNAi). (Rate:
6 Votes
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)
- siRNA at Whitehead
(Whitehead Institute for Biomedical Research)
- 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. (Rate:
3 Votes
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) - siRNA Design
(Integrated DNA Technologies)
- Design siRNA following the rules of either T. Tuschl or A. Fire. Accept accession number or sequence as input. No database blasting. (Rate:
2 Votes
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)
- siRNA Target Finder
(GenScript)
- Find siRNA target. Acceptable input are accession number and sequence. Five databases including human, mouse, rat and drosophila are available for blasting. (Rate:
3 Votes
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) - TROD: T7 RNAi Oligo Designer
(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. (Rate:
0 Votes
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