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WMD / Web MicroRNA Designer
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 small RNA from endogenous miRNA precursors. WMD3 was initially implemented for Arabidopsis thaliana, but has now been extended to more than 30 additional species for which genome or extensive EST (expressed sequence tag) information is available. WMD3 is designed to optimize both intrinsic small RNA properties as well as specificity within the given transcriptome.
dsCheck
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 scan for each siRNA to find off-target gene candidates, simulating the biochemical process of dsRNA-mediated RNAi in vivo. dsCheck also provides efficient design of ‘off-target minimized’ dsRNA by avoiding regions that share a considerable number of diced siRNAs with a specific off-target gene, and monitoring the total number of off-target hits.
P-SAMS / Plant Small RNA Maker Site
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 plants. P-SAMS includes two applications, P-SAMS amiRNA Designer and P-SAMS syn-tasiRNA Designer. The navigation through both applications is wizard-assisted, and the job runtime is relatively short. Both applications output the sequence of designed small RNA(s), and the sequence of the two oligonucleotides required for cloning into 'B/c' compatible vectors.
SDS / siRNA Design Software
Assists users in the design of short interfering RNAs (siRNAs) for silencing gene expression. SDS filters potential ineffective siRNA candidates from the output of existing tools. The software is based on the secondary structure properties, called repelling loops and big repelling loops. The rule for classifying potential ineffective siRNAs from other candidates is generated with the help of artificial intelligence (AI) techniques, in particular, the decision tree and support vector machine.
UP-TORR / Updated Targets of RNAi Reagents
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 current information available, and for Drosophila, also synchronizes with the major reagent collections. Thus, UP-TORR allows users to choose the most appropriate RNAi reagents at the onset of a study, as well as to perform the most appropriate analyses of results of RNAi-based studies.
imRNA
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 prediction models using various features that include composition-based features, binary profile, selected features, and hybrid features. All models were evaluated using five-fold cross-validation and external validation techniques; achieving a maximum mean Matthews Correlation Coefficient of 0.86 with 93% accuracy.
MicroLive
Assists virologists in designing potential miRNA response elements (MREs). MicroLive was developed to construct safer live attenuated virus vaccines. It includes a web server that enables users to interactively find and optimize the potential MREs for a specific human miRNA within users’ input viral sequences of interest. This resource can also be applied to design MREs for engineering tissue-specific oncolytic viruses or for constructing live attenuated virus vaccines for other hosts of interest such as animals.
AmiRNA Designer
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 contrast to the available automated tools, AmiRNA Designer program allows the user to perform analysis of natural miRNAs for the organism of interest and to create customized constraints for the design stage. It also provides filtering of the amiRNA candidates for the potential off-targets.
SPICE / shRNA target prediction informed by comprehensive enquiry
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 well as information associated with each gene. It executes several tasks: (i) identification of siRNA sequence region in vector harboring shRNA-encoding DNA, (ii) sequence alignment between passenger strand of the siRNA and human RefSeq DNA database, (iii) functional annotation of the siRNA target DNA using databases, (iv) calculation of Gene Expression Omnibus (GEO) profile data to show significant microarray experiments in humans, and (v) preparation of downloadable summary files to support spreadsheet database construction in a local personal computer.
OfftargetFinder
Obsolete
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 do not contain 21mer matches with a library of over 100 arthropod transcriptomes. It can therefore be used to design RNAi pesticides likely to have a narrow spectrum of affected species. 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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