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AMOD -- a morpholino oligonucleotide selection tool
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| Select an oligonucleotide for design of an antisense morpholino against a target nucleotide sequence. |
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AOBase -- a database for antisense oligonucleotides selection and design
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| Search for published antisense oligonucleotides (ODNs).
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ASRP -- the Arabidopsis Small RNA Project database
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| Search for information on Arabidopsis endogenous small RNAs - microRNAs (miRNAs) and short-interfering RNAs (siRNAs). |
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Ambion GeneAssist™ Pathway Atlas
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| Learn how a protein is involved in different cellular pathways. |
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AntiHunter 2.0 -- increased speed and sensitivity in searching BLAST output for EST antisense transcripts
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| Detect potential EST antisense transcripts within a given genomic region.
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AsiDesigner -- exon-based siRNA design server considering alternative splicing
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| An siRNA design program based on exon-based siRNA design algorithm considering alternative splicing.
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CMGSDB -- integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining
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| The Database for Computational Modeling of Gene Silencing is an integration of heterogeneous data sources about C. elegans with capabilities for compositional data mining across diverse domains.
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CSRDB -- a small RNA integrated database and browser resource for cereals
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| Search for sequence information on rice, maize and other cereal crops small RNAs. |
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CoGemiR -- a comparative genomics microRNA database
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| Provides an overview of the genomic organization of microRNAs and extent of conservation during evolution in different metazoan species.
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CrossLink -- visualization and exploration of sequence relationships between (micro) RNAs
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| Analyze sequence relationships between microRNAs.
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DEQOR -- A Web-based Tool for the Design and Quality Control of siRNAs
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| Design siRNAs for RNAi with quality control.
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Dharmacon siDESIGN Center
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| Design siRNA targets using Dharmacon's online siDESIGN Center.
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E-RNAi -- a web application to design optimized RNAi constructs
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| Evaluate and design optimized dsRNA constructs.
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FLIGHT -- database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets
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| Browse and cross-correlate data from large-scale RNAi studies using Drosophila cell lines. |
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FlyRNAi -- the Drosophila RNAi screening center database
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| Search for Drosophila RNAi screening data. |
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GenomeRNAi -- a database for cell-based RNAi phenotypes
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| Search for information on RNAi induced cell-based Drosophila and Caenorhabditis elegans phenotypes.
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HuSiDa -- the human siRNA database -- an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells
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| Search for sequences of published functional siRNA molecules targeting human genes and associated information. |
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MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.
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| Distinguish between real and pseudo microRNA precursors
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MiRFinder -- microRNA finder
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| An improved approach and software implementation for genome-wide fast microRNA precursor scans.
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MicroRNA.org -- targets and expression resource
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| Find microRNA target predictions and expression profiles in this comprehensive resource.
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Mireval -- Sequence evaluation of microRNA properties
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| A web tool for simple microRNA prediction in genome sequences.
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NATsDB -- Natural Antisense Transcripts DataBase
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| Search for natural antisense transcripts (NATs) in human, mouse, fly and other eukaryotic genomes.
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OligoWalk -- an online siRNA design tool utilizing hybridization thermodynamics
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| An online sever calculating thermodynamic features of sense-antisense hybridization.
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PhenomicDB -- Comparison of phenotypes of orthologous genes in human and model organisms
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| Compare phenotypes of a given gene or gene set in different model organisms. |
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PolymiRTS Database -- linking polymorphisms in microRNA target sites with complex traits
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| Search for naturally occurring DNA variations in putative microRNA target sites. |
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ProMiR II -- a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs
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| Predict miRNA genes.
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RFRCDB-siRNA -- Design of siRNA with Random Forest Regression Model Coupled with Database Searching
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| Predict siRNA efficacy.
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RNAdb —- a comprehensive mammalian noncoding RNA database
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| Search for information on experimentally studied mammalian non-coding RNAs (ncRNAs), including many associated with diseases and/or developmental processes. |
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RNAhybrid -- microRNA target prediction easy, fast and flexible
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| Predict multiple potential binding sites of miRNAs in large target RNAs.
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RNAi Codex -- a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs
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| Search for shRNA related information and website.
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RNAiDB and PhenoBlast -- Web Tools for Genome-Wide Phenotypic Mapping Projects
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| Archive, distribute and analyze phenotypic data from large-scale RNAi analyses in Caenorhabditis elegans. |
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Sfold --Statistical Folding and Rational Design of Nucleic Acids
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| Design RNA-targeting nucleic acids, which include small interfering RNAs (siRNAs), antisense oligonucleotides and trans-cleaving ribozymes for gene knock-down studies.
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TROD -- T7 RNAi Oligo Designer
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| Design oligodeoxynucleotide sequences for the in vitro production of siRNA duplexes with T7 RNA polymerase.
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ViTa -- prediction of host microRNAs targets on viruses
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| Search for curated information of the known virus miRNA genes and the known/putative target sites of human, mice, rat and chicken miRNAs. |
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Vir-Mir db -- prediction of viral microRNA candidate hairpins
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| Predict viral miRNA hairpins.
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dsCheck -- highly sensitive off-target search software for double-stranded RNA-mediated RNA interference
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| Estimate off-target effects by the long double-stranded RNA used in RNAi studies.
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miRAS -- miRNA Analysis System
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| A data processing system for miRNA expression profiling study.
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miRBase -- tools for microRNA genomics
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| Search for comprehensive microRNA sequence data, annotation and predicted gene targets.
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miRDB -- MicroRNA Database
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| A microRNA target prediction and functional annotation database with a wiki interface.
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miRGator -- an integrated system for functional annotation of microRNAs
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| Database and navigator tool for functional interpretation of miRNAs.
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miRGen -- a database for the study of animal microRNA genomic organization and function.
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| Search for information on non-annotated/unannotated non-coding mRNA transcripts.
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miRNAMap 2.0 -- genomic maps of microRNAs in metazoan genomes
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| Search for information on the published and predicted miRNA in vertebrate genomes. |
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miRNApath -- a database of miRNAs, target genes and metabolic pathways
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| Provides data about mature miRNAs, miRNAs targets, and the pathways that they are involved.
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ncRNAdb -- Noncoding regulatory RNAs database
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| Search for sequence and other information about noncoding regulatory RNAs. |
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siDRM -- an effective and generally applicable online siRNA design tool
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| Select effective siRNAs.
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siDirect -- Target-specific siRNA Design Software for Mammalian RNA Interference
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| Design small interfering RNA (siRNA) sequences with maximum target-specificity for mammalian RNA interference.
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siRNA Design (Qiagen)
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| Design siRNA by sequence or by GenBank accession number.
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siRNA Design Tool (Wistar Institute)
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| Scan a target gene sequence from human, mouse fly or rat for candidate siRNA sequences.
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siRNA Selection Server -- an automated siRNA oligonucleotide prediction server
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| Identify potential siRNA target sites within an mRNA sequence.
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siRNA Sequence Selector (Clontech)
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| Generate candidate siRNA sequences.
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siRNA Target Designer (Promega)
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| Analyzes the input sequence and find regions within that sequence which fit the siRNA Target Design Parameters.
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siRNA Target Finder (GenScript)
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| Identify siRNA target sites for an mRNA or cDNA molecule.
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siRNA target finder (Ambion)
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| Identify potential siRNA target sites within an mRNA sequence and then generates the sequences of the corresponding siRNAs.
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siRNAdb -- a database of siRNA sequences
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| Take a gene-centric view of siRNA experimental data.
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siRecords -- Small Interfering RNA Experiments Database
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| A database of experimentally validated mammalian siRNAs with efficacy ratings.
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siVirus -- web-based antiviral siRNA design software for highly divergent viral sequences
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| Conduct efficient antiviral siRNA design.
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