An open-source software package for predicting microRNA target site variants (miR-TSVs) from clinical genomic data sets that measure miRNA expression, gene expression, and genotype. The main benefits of SubmiRine are that it allows for de novo prediction of miR-TSVs from custom data sets - such as those that can be generated from large-scale clinical genomics projects - and provides a methodology to prioritize predicted miR-TSVs by their relative probability of being functional. Thus, SubmiRine enables researchers to perform miR-TSV prediction efficiently and systematically on genome-scale data sets and narrow down the list of candidates to a manageable set for further validation.
Calculates features of metastable conformations determined by putative miRNA binding sites. MSbind is a Perl package that sorts meta-stable structures by number of base pairings within the target site. It approximates the opening energies of meta-stable target sites using RNAeval. It also averages the opening energy and depth of meta-stable structures.
Predicts the impact of a SNP on putative microRNA targets. MicroSNiPer interrogates the 3'-untranslated region and predicts if a SNP within the target site will disrupt/eliminate or enhance/create a microRNA binding site. This application computes these sites and examines the effects of SNPs in real time. MicroSNiPer is a user-friendly Web-based tool. Its advantages include ease of use, flexibility, and straightforward graphical representation of the results.