Rank miRNA: a web tool for identifying polymorphisms altering miRNA target sites

MicroRNAs (miRNAs) are small non-coding RNA molecules that have an important role in a wide range of biological processes, since they interact with specific mRNAs affecting the expression of the corresponding proteins. The role of miRNA can be deeply influenced by Single Nucleotide Polymorphisms (SNPs), in particular in their seed sites, since these variations may modify their affinity with particular transcripts, but they may also generate novel binding capabilities for specific miRNA binding sites or destroy them. Several computational tools for miRNA-target site predictions have been developed, but the obtained results are often not in agreement, making the study the binding sites hard, and the analysis of SNP effects even harder. For these reasons, we developed a web application called Rank miRNA, which allows to retrieve and aggregate the results of three prediction tools, but also to process and compare new input miRNA sequences, allowing the analysis of how variations impact on their function. Therefore, our tool is also able to predict the impact of SNPs (and any other kind of variations) on miRNA-mRNA binding capability and also to find the target genes of (potentially new) miRNA sequences. We evaluated the performance of Rank miRNA on specific human SNPs, which are likely to be involved in several mental disorder diseases, showing the potentiality of our tool in helping the study of miRNA-target interactions.