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.
