1. Annotating a new genome based on miRNAs known from other species, in the absence of any small RNA expression.
2. Prefiltering entries from miRBase to a subset of loci whose predicted structures conform to accepted criteria.
Importantly, the results for miR_homologs.pl can be fed into ShortStack in --count mode, in order to compare MIRNA loci identified by homology to actual expression data.