For each putative or known miRNA, user may query the target sites in the 3'UTR regions of genes of human, mouse, rat, zebrafish, rice or Arabidopsis. From the human.rna.fna file downloaded from NCBI, we fetched the sequences of human 3'UTRs based on the CDS (coding sequence) positions acquired from the human.rna.gbff file. We adopted the same strategy for the mouse, rat, zebrafish, rice and Arabidopsis 3'UTRs.
When operating RNAhybrid, the pipeline first calculates the optimal free energy of miRNA at which it binds to a perfectly complementary site, then the miRNA/mRNA duplex mfe (minimum free energy). An alignment whose RNA duplex mfe is more than the selected percentage of its correspondent optimal free energy is regarded as a positive alignment. The alignment result will be sent to the users via their e-mail addresses. We greatly appreciate Dr. Rehmsmeier for providing the RNAhybrid program.
For further information:
If you have question on RNAhybrid, please refer to "Fast and effective prediction of microRNA/target duplexes". If you have question on RNA duplex mfe, please refer to "Combinatorial microRNA target predictions".