miRU

miRU is a software tool developed for predicting plant miRNAs' potential targets through computational sequence similarity search. The tool is web-based and integrated, making it accessible to any plant species as long as many sequences are available.

The tool performs a thorough search for potential complementary target sites with mismatches that are tolerable in miRNA-target recognition, given a mature miRNA sequence from a plant species. True or false positives are estimated based on the number and type of mismatches in the target site, as well as on the evolutionary conservation of target complementarity in another genome, which can be selected according to miRNA conservation.

The output for predicted targets is ordered by mismatch scores and includes complementary sequences with mismatches highlighted in colors, original gene sequences, and associated functional annotations. This feature offers a comprehensive view of the predicted targets and their possible functions, which can be valuable for further experimental validation.