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

Databases	Description
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
SiRecords	Mammalian siRNA records tested and evaluated by research laboratories also find good siRNAs targeting a particular gene.
siRNAdb	A database of known siRNA molecules.
RNAi Codex	Collection of shRNA libraries of different organism like, H. sapiens, M, musculus, Rattus norvegicus, and A. thaliana.
HuSiDA	Human siRNA database

siRNA design

These are some tools, which can be helpful to design siRNA for a specific gene.

Academic	Description
siRNA at Whitehead	It helps in selecting siRNAs to knock down the gene of interes.
siRNA selector	program evaluates siRNA FUNCTIONALITY and SPECIFICITY
siDirect	highly effective, target specific siRNA online design site

Commercial	Description
Ambion	siRNA Target Finder
Dharmacon siDESIGN	an advanced, user-friendly siRNA design tool, which significantly improves the likelihood of identifying functional siRNA.
QIAGEN	Products 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
TripletSVM	Predict 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.
BayesmiRNAfind

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.