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RNAi reagent design software tools | RNA interference

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…
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RNAxs
Web

RNAxs

Helps you to design potent siRNAs to knock down your gene(s) of interest. RNAxs…

Helps you to design potent siRNAs to knock down your gene(s) of interest. RNAxs is based on the RNAplfold program to assess the mRNA target site accessibility. RNAxs was trained on two different…

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AmiRNA Designer
Desktop

AmiRNA Designer

A tool dedicated to design artificial micro RNAs (amiRNA and amiRNA*…

A tool dedicated to design artificial micro RNAs (amiRNA and amiRNA* sequences). AmiRNA Designer is based on the thermodynamic analysis of the native miRNA/miRNA* and miRNA/target duplexes. In…

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WMD
Web
Desktop

WMD Web MicroRNA Designer

Automates artificial microRNAs (amiRNAs) design. WMD3 uses the favorite…

Automates artificial microRNAs (amiRNAs) design. WMD3 uses the favorite gene(s), which the user want to silence, and designs 21mer amiRNA sequences. User will retrieve oligo sequences to express the…

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OfftargetFinder
Web

OfftargetFinder

Searches the ever-growing arthropod transcriptome databases so that…

Searches the ever-growing arthropod transcriptome databases so that pest-specific RNAi sequences can be identified. The web tool OfftargetFinder can be used to identify stretches of nucleotides that…

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P-SAMS
Web

P-SAMS Plant Small RNA Maker Site

A web tool for the simple and automated design of artificial miRNAs (amiRNAs)…

A web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in…

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SMEpred…
Web

SMEpred workbench

A web server for predicting efficacy of chemically modified siRNAs. SMEpred…

A web server for predicting efficacy of chemically modified siRNAs. SMEpred workbench is used to predict the efficacy of normal siRNAs as well as cm-siRNAs using 3031 heterogeneous cm-siRNA sequences…

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miR-Synth
Web

miR-Synth

A computational resource for the design of synthetic miRNAs (a-miR) able to…

A computational resource for the design of synthetic miRNAs (a-miR) able to target multiple genes in multiple sites. miR-Synth combines well-established knowledge on miRNA targeting together with…

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AsiDesigner
Web

AsiDesigner

A web-based siRNA design software system, which provides siRNA design…

A web-based siRNA design software system, which provides siRNA design capability to account for alternative splicing for mRNA level gene silencing.

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OligoWalk
Web

OligoWalk

An online server calculating thermodynamic features of sense-antisense…

An online server calculating thermodynamic features of sense-antisense hybridization.

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Sirna
Web

Sirna

Target accessibility prediction and RNA duplex thermodynamics for rational…

Target accessibility prediction and RNA duplex thermodynamics for rational siRNA design.

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siSPOTR
Web

siSPOTR

This tool allows researchers to determine the off-targeting potential for…

This tool allows researchers to determine the off-targeting potential for siRNAs they have already designed.

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OptiRNA
Web

OptiRNA

A practical, freely accessible and transparent web app for the identification…

A practical, freely accessible and transparent web app for the identification of target sites with over 90% knockdown activity. OptiRNA supports vector machines with polynomial kernels and…

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Deqor
Web

Deqor

Predicts the probability that an mRNA fragment will cross-react with other…

Predicts the probability that an mRNA fragment will cross-react with other genes in the cell and helps researchers to design experiments to test the specificity of esiRNAs or chemically designed…

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E-RNAi
Web

E-RNAi

A tool for the design and evaluation of RNAi reagents for a variety of species.

A tool for the design and evaluation of RNAi reagents for a variety of species.

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SPICE
Web

SPICE shRNA target prediction informed by comprehensive enquiry

A web-based analysis and search tool for investigating biological information…

A web-based analysis and search tool for investigating biological information about shRNA sequences using random oligonucleotides. SPICE displays target candidate genes with sequence alignment as…

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imRNA
Web

imRNA

A web server for designing a single-stranded RNA (ssRNA) sequence with desired…

A web server for designing a single-stranded RNA (ssRNA) sequence with desired immunomodulatory potentials, for designing RNA-based therapeutics, immunotherapy and vaccine adjuvants. We developed…

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BiLTR
Desktop

BiLTR

A generic framework to enhance siRNA knockdown efficacy prediction. The key…

A generic framework to enhance siRNA knockdown efficacy prediction. The key idea is first to enrich siRNA sequences by incorporating them with rules found for designing effective siRNAs and…

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DSIR
Web

DSIR Designer of Small Interfering RNA

A linear model for siRNA prediction and shRNA target design. DSIR performs as…

A linear model for siRNA prediction and shRNA target design. DSIR performs as well as more complex state-of-the-art models in terms of potency prediction accuracy, with the advantage of being…

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siDRM
Web

siDRM

Helps in selecting effective Small interfering RNAs (siRNAs). siDRM is a…

Helps in selecting effective Small interfering RNAs (siRNAs). siDRM is a full-featured siRNA design tool in which several improved DRM rule sets are implemented. It includes the incorporation of a…

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UP-TORR
Web

UP-TORR Updated Targets of RNAi Reagents

An online tool useful for accurate and up-to-date annotation of cell-based and…

An online tool useful for accurate and up-to-date annotation of cell-based and in vivo RNAi reagents. Importantly, UP-TORR automatically synchronizes with gene annotations daily, retrieving the most…

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siRNArules
Desktop

siRNArules

An open-source JAVA program that is surprisingly efficient at predicting active…

An open-source JAVA program that is surprisingly efficient at predicting active siRNAs.

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desiRm
Web

desiRm

Helps to make siRNA of desired efficacy without changing the target site.…

Helps to make siRNA of desired efficacy without changing the target site. desiRm is a webserver for designing highly effective siRNA for silencing a gene. This tool is a method to design siRNA…

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MysiRNA-designe…
Desktop

MysiRNA-designer

Integrates several factors in an automated work-flow considering mRNA…

Integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.

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siRNA design
Web

siRNA design

Allows users to upload their gene fusion sequences. sIRNA design provides an…

Allows users to upload their gene fusion sequences. sIRNA design provides an interface where siRNA sequences can be designed using a combination of four prediction tools namely RNAxs, BiLTR, siDirect…

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BLOCK-iT RNAi…
Web

BLOCK-iT RNAi Designer

A web-app for the design of Stealth RNAi™ siRNA. For three best Stealth…

A web-app for the design of Stealth RNAi™ siRNA. For three best Stealth RNAi™ siRNA sequences designed by the BLOCK-iT™ RNAi Designer, two of them give greater than 70% knockdown of mRNA, given…

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siDESIGN Center
Web

siDESIGN Center

An advanced, user-friendly siRNA design tool, which significantly improves the…

An advanced, user-friendly siRNA design tool, which significantly improves the likelihood of identifying functional siRNA.

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SnapDragon
Web

SnapDragon

A web-based tool for the design of long dsRNAs for specific gene knockdown in…

A web-based tool for the design of long dsRNAs for specific gene knockdown in Drosophila melanogaster via an RNAi approach.

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dsCheck
Web

dsCheck

A web app for estimating off-target effects caused by the long double-stranded…

A web app for estimating off-target effects caused by the long double-stranded RNA (dsRNA) used in RNAi studies. dsCheck dices the input sequence into an siRNA cocktail and performs an exhaustive…

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siVirus
Web

siVirus

A web-based online software system that provides efficient short interfering…

A web-based online software system that provides efficient short interfering RNA (siRNA) design for antiviral RNA interference (RNAi).

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siDirect
Web

siDirect

Provides functional and off-target minimized siRNA design for mammalian RNAi.

Provides functional and off-target minimized siRNA design for mammalian RNAi.

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