miRNAminer: A tool for homologous microRNA gene search

An algorithm we developed – miRNAminer – is used for homologous conserved miRNA gene search in several animal species. Given a search query, candidate homologs from different species are tested for their known miRNA properties, such as secondary structure, energy and alignment and conservation, in order to asses their fidelity. When applying miRNAminer on seven mammalian species we identified several hundreds of high-confidence homologous miRNAs increasing the total collection of (miRbase) miRNAs, in these species, by more than 50%. miRNAminer uses stringent criteria and exhibits high sensitivity and specificity.We present – miRNAminer – the first web-server for homologous miRNA gene search in animals. miRNAminer can be used to identify conserved homolog miRNA genes and can also be used prior to depositing miRNAs in public databases. miRNAminer is available at http://pag.csail.mit.edu/mirnaminer webcite.MicroRNAs (miRNAs) are short, ~22 nt non-coding RNAs that control gene expression. miRNAs bind to the 3'UTRs of their regulated mRNA transcripts to facilitate mRNA degradation or translation inhibition [1,2]. miRNAs are present in most metazoans and are thought to regulate a diverse range of biological processes [3,4]. miRNA genes' evolution is unique since they mostly emerge through duplication events [5]; exhibit most often unidirectional evolution [6]; are generally gained and not lost [7]; show several cases of rapid evolution in primates [8,9]; are rarely changed due to functional constraints [10]; and, show relatively rare evolutionary acquisition events (accounted by their relatively small numbers).miRNA predictions based on computational methods, which followed initial extensive cloning efforts, are based on the secondary structure of the miRNA, its phylogenetic conservation and thermodynamic stability [11,12]. miRNA gene repositories are constantly expanding giving rise to more than 3500 reported miRNAs in more than 30 animal species (Sanger miRbase database