MicroRNAs (miRNAs) are about 22-nucletide-length endogenous non-coding RNA molecules that suppress target gene expression. Functional miRNAs typically form RNA-induced silencing complexes (RISCs) that hybridize complementary sequences at 3'-untranslated regions (3' UTRs) of target genes to either degrade mRNA molecules or suppress protein translation . In animals and plants, miRNAs regulate many cellular processes including cell proliferation, differentiation, apoptosis and development . miRNA regulation could be the etiological factor of many diseases including cancer, as well as neurological, and cardiovascular disorders . Biologists have discovered that, on each miRNA, the second to seventh nucleotides (position 2-7) called "seed region" is indispensable for miRNA-target interactions (MTIs) . The seed region in miRNAs should match with the 3' UTR sequence complementarily. So far, the conventionally approaches to verify MTIs such as the reporter assay are still time consuming and incapable of handling the large-scale screening.
Recent works demonstrated that the novel miRNAs, miRNA expression, or MTIs can be uncovered in a large scale by using the next-generation sequencing (NGS) technology. For example, miRDeep  predicts the novel miRNAs in NGS data according to a probabilistic model of miRNA biogenesis. Its newest version, miRDeep2 , reaches the accuracy around 98.6%-99.9%. Additionally, several tools or web servers were used to identify novel miRNAs or detect miRNA expression levels via NGS such as deepBase , Geoseq , miRanalyzer , SeqBuster , mirTools , DSAP , miRNAkey  and miRExpress .
Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) was used to identify specific protein-RNA interaction. Functional miRNA was loaded into Argonate protein and then bound to their target gene to slicing gene expression. Hence the function of Argonate-mRNA-miRNA complex can be verified through CLIP technology. Nowadays, ChIP-seq technology study in protein-DNA interaction by high-throughput sequencing, CLIP-seq technology has been developed to identify protein-RNA interaction by high-throughput sequencing. In 2009, Chi et al. pioneered the use of crosslinking and immunoprecipitation (CLIP) method combining with the next-generation sequencing (NGS) technology to discover MTIs in order to obtain Argonaute proteins with mRNA molecules (i.e., targets) in mouse brain. Furthermore, Hafner et al.  developed a modified CLIP method, namely Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), to enhance the resolution of the original CLIP method. PAR-CLIP enhances protein-RNA crosslinking by introducing photoactivatable ribonucleoside (4-thiouridine, 4SU) into RNAs, makes RNAs sustain in ultra-violet light (UV) with higher energies. Thus, tighter binding was created and results in higher efficiency of RNA co-immunoprecipitation. However it also leads to T to C conversion in the miRNA-RNA-protein crosslinking regions due to the fact that thymine tends to be replaced by 4SU, which could be misidentified as cytosine.
Recently, more and more research groups investigated large-scale MTIs using the CLIP-seq [17–20], and there are several databases, such as CLIPZ , starBase , doRiNA , and TarBase 6.0 , compile public available CLIP and PAR-CLIP sequencing datasets and use their in-house software toolkits to analyze the raw data. Among them, only the CLIPZ provides a free web-based analytics environment to the public, and users have to upload their data to the server, which is impractical due to the huge size of the raw sequences and the limited internet bandwidth. Regarding to standalone tools, PARalyzer  is the only one that focuses on PAR-CLIP dataset analysis so far, and its execution time is not satisfactory. In other words, there are only two public available tools that are capable of analyzing CLIP and PAR-CLIP sequencing data, and none of them were designed specifically for MTIs.
We herein propose the first CLIP and PAR-CLIP sequencing analysis platform specifically for miRNA target analysis, namely miRTarCLIP. We devised a unique C to T reversion in its workflow to significantly reduce its running time, and included other novel features (see below), which increase miRTarCLIP's functionality. In addition, miRTarCLIP serves with a web-based interface to provide better user experiences in browsing and searching targets of interested miRNAs.