An application to quantify and annotate miRNA expression.
microRNAs (miRNAs) are an important class of small noncoding RNAs (~22nt) with multiple and widespread regulatory roles in many development and disease processes. We have created the tool Prost! to explore metazoan miRNA-enriched RNA-Seq data. Prost! quantifies and normalizes expression levels (in the form of Illumina reads) in several views that are suitable as input into differential expression software such as DESeq2. Some key features of Prost! include the identification of both candidate mirror-miRNAs and putative 5 ́/3 ́ mature miRNA arm switching. Of particular interest is the tightly regulated post-transcriptional modification of miRNAs via multiple modes of regulation during their biogenesis. Such modifications have been found to have important consequences on characteristics such as Argonaute loading, target choice, and miRNA turnover. Prost! provides valuable quantification across samples of several classes of miRNA modifications, for example putative seed shifting, seed editing, and untemplated 3 ́ nucleotide additions.