RNA interference

RNAinterference (RNAi) is an evolutionary conserved, gene silencing mechanism mediated through small non-coding RNA. It plays a significant role in the development of organism and also maintains the integrity of the genome. The RNAi pathway is complex that is triggered by double stranded RNA (dsRNA). The enzyme Dicer process the dsRNA to generate 20-25 bp fragments and one of the two strand of the fragment bind to the RISC (RNA-induced silencing complex) that subsequently bind to the mRNA in sequence specific manner to degrade the mRNA. The short 20-25 bp fragments are known as small interfering RNA (siRNA) when they are produced from dsRNA and microRNA (miRNA) when they are produced endogenously as hairpin loop structure. RNAi has become a valuable research tool to knock down a specific gene to study the function of a gene. In addition to research applications it is also emerging as a novel therapeutic intervention to suppress disease causing genes. To use this natural mechanism for human benefit it is crucial to understand the basic mechanism of RNAi and its associated components. Information about resources, which can be utilized to make RNAi technology more effective are given below:

Database of miRNA

These are some database, which provide information about miRNA gene, and its expression profile in different tissues.
Database Description
miRBase A database of miRNA, provide names for novel miRNA genes prior to publication. Also predicted miRNA targets in animals by using the tools, MIRNANDA and TARGETSCAN.
miRNAMap A database of experimental verified microRNAs and its target genes in human, mouse, rat, and other metazoan genomes. Also provides expression profile of miRNA in tissue specific and differential expression in cancer/normal cell.
ASRP Repository for sequences of small RNAs (microRNAs and siRNA) cloned from various Arabidopsis thaliana genotypes and tissues.
miRNApath A database of miRNAs, target genes and metabolic pathways.
miRGen A database of cluster of miRNA, genomics and their targets.
miRex Serves an online repository for microRNA gene expression data and also analyses the microRNA expression data.
ARGONAUTE2 A database on mammalian microRNAs and their function in gene and pathway regulation.

Database of miRNA target

TarBase A database of experimentally supported animal microRNA targets.

Database of siRNA

These are some database, which can be used to know the siRNA for a gene, and also the gene, which can be targeted by a effective siRNA.
Database Description
SiRecordsMammalian siRNA records tested and evaluated by research laboratories also find good siRNAs targeting a particular gene.
siRNAdbA database of known siRNA molecules.
RNAi CodexCollection of shRNA libraries of different organism like, H. sapiens, M, musculus, Rattus norvegicus, and A. thaliana.
HuSiDAHuman siRNA database

siRNA design

These are some tools, which can be helpful to design siRNA for a specific gene.
Academic Description
siRNA at WhiteheadIt helps in selecting siRNAs to knock down the gene of interes.
siRNA selectorprogram evaluates siRNA FUNCTIONALITY and SPECIFICITY
siDirecthighly effective, target specific siRNA online design site

Commercial Description
AmbionsiRNA Target Finder
Dharmacon siDESIGNan advanced, user-friendly siRNA design tool, which significantly improves the likelihood of identifying functional siRNA.
QIAGENProducts and services for life science research, molecular diagnostics, genomics, and gene therapy

miRNA predition tool

These are some tools, which can be used to predict the potential miRNA precursors. i
Tools Description
TripletSVMPredict whether the query hairpin structure is a real miRNA precursor or not.
miR-abela miRNA gene prediction.
MIRScan Predict miRNA precursors.
MiRAlign Predict hairpin containing mature miRNA in animals and plants.
RNAmicro Predict microRNA precursors in comparative genomics data.
findMIRNA Predicting miRNA precursor candidates in A. thaliana.

miRNA target prediction tools

Tools Description
miRacle miRNA target prediction.
miRanda Predict miRNA targets and also provides the expression profile of miRNA in various tissues.
RNAhybrid Hybridize a long and a short RNA.
TragetScan Predict miRNA (miRNA family) target in vertebrates, worm, and fly.
MicroInspector Detect miRNA binding sites in an mRNA sequence.
Pic Tar Predict miRNA target in vertebrates , flies, and nematodes.
miRNA-Target predict Predict Drosophila miRNA targets.
DIANA Micro Test miRNA target prediction.
miRU Predict plant miRNA target.
TargetBoost Predict miRNA target in C.elegans.
RNA22 A pattern-based method for the identification of microRNA-target sites and their corresponding RNA/RNA complexes.