I've acquired a set of NGS data, human RNA. There are suspected SNPs, which I have reason to believe could either hinder miRNA:RNA interaction or create new miRNA:RNA interaction site.
Therefor my plan is to gather sequences from around the SNPs (20bp up/downstream) and input them to a prediction tool which could asses which if any miRNAs could potentially interact with it. Conversely if I input the reference (no newly discovered SNPs), which miRNAs would interact with this site, namely which miRNA potentially lost its effect of the transcript.
What would be a good way of doing this?