What is miRTar?
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      miRTar is a web server which provides an intuitive interface to allow user input any miRNA/siRNA sequence for identifying miRNA targets against the 3'-UTR of mRNA of mammalian genes. The main advantage of the web server comparing to previously developed tools (see references) is the efficient performance. Thus, the miRNA/siRNA targets search becomes faster enough to be a web server.
      miRTar incorporates a preprocessing algorithm, named iScan, and a powerful miRNA targets search tool, miRanda, to search the miRNA targets against the most conserved 3'-UTR sequences from UCSC Genome Browser.
      The flowchart as follow:

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miRTar performs more efficiently
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      To compare the efficiency of miRanda and miRTar (IScan + miRanda), we test a miRNA "hsa-let-7a" in the two systems to predict its targets in human conserved 3'UTR and check the time cost in different minimum free energy, MFE (fixed score >=160) and different score (fixed MFE <= -18).
      The data size of 3' UTR is about 24M, if we use miRanda directly, the time cost is about 100 seconds and the data size of miRNA targets in 3' UTR is about 3K, but if we use miRTar, which can quickly filter out lots of unlikely miRNA target regions, and then the data size of 3'UTR will remain about 2.2M and the total time cost is faster, less than 20 seconds.
      The illustration and results as presented as follows.

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Tutorial
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In the home page, please click "Prediction" and into the predict miRNA targets format.
The Predicting Submission
Step 1: User should give a (a) miRNA accession number (given by miRBase) or (b) miRNA/siRNA sequence (FASTA format only!). Such as hsa-let-7a-1, hsa-miR-23a, and so on. Step 2: Seclect the miRNA targets of human, mouse or rat. Step 3: Seclect the miRNA targets of 3'-UTR, 5'-UTR or CDS(coding sequence). Step 4: Set the parameters or use the default value: (1) hybridization temperature 37 ° C. (2) minimum free energy <= -18 kcal / mol. (3) score >= 160. Recommended parameters Species Hybridizaion temperature Minimum free energy cut-off Score cut-off Homo sapiens 37 ° C -18 160 Mus musculus 37 ° C -18 160 Rattus norvegicus 37 ° C -18 160
The Results
E2: The free energy of the original target mRNA secondary structure.
E4: The free energy of the target mRNA secondary structure after miRNA binding.

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