Welcome to ZooMir Database

ZooMir is an online database of homologous microRNA search in animal genomes.

MicroRNAs (miRNAs) are endogenous non-protein-coding RNAs of ~22 nucleotides. Since the initial discovery of miRNAs in Caenorhabditis elegans (C. elegans) , thousands have been identified (computationally and/or experimentally) in many organisms, including mammals, invertebrates, insects, plants and viruses, which suggests that miRNA genes have been conserved during evolution and widely distributed among species. Here, we modified our previous pre-miRNA discovery pipelines to predict miRNAs in 50 metazoan genomes.

Because the highly conserved nature of miRNAs in evolution is significant for prediction accuracy, we modified the miRNA discovery pipeline by implementing an initial search for conserved mature miRNA sequences in available genomes to increase the prediction accuracy. The conservation filter was first used to locate evolutionarily conserved miRNA-like fragments. Then, we checked whether or not the sequences adjacent to the miRNA-like fragments could fold into hairpins. We implemented the modified discovery pipeline to detect mature miRNAs and pre-miRNAs in 50 animal genomes obtained from UCSC Genome Bioinformatics web site (http://www.genome.ucsc.edu/).

We then calculated the values of selected quantifiable features from the resulting pool of potential miRNAs and used them as discriminating indices in the Support Vector Machine (SVM) algorithm. Using the classifier trained by SVM, we identified 17,479 novel orthologous or paralogous pre-miRNAs, as well as their putative corresponding mature miRNAs, using 1,901 sequentially unique miRNA patterns collected from the miRBase. By reversing the conservation and hairpin finding procedures, we achieved excellent miRNA discovery with 89.5% sensitivity and 97.4% specificity.

Our results suggest that miRNA genes are widely distributed in many animal species, including Schmidtea, nematode, insect, urchin, sea squirt, and vertebrates. Different miRNA classes have distinct distribution patterns among these species, which may provide insight into miRNA evolution and their functional significance in development and organogenesis.

Please Cite as:Li SC, Chan WC, Hu LY, Lai CH, Hsu CN and Lin WC, Identification of homologous microRNAs in 56 animal genomes, Genomics, 96(1):1-9.