I am trying to generate an estimate of the number of microRNA targets of several orthlogus miRNAs across a set of animal species. Specifically, I want to produce an estimated number of targets for each (species,miRNA) pair, using the intersection of the outputs of several target prediciton tools which I will run against the miRNA sequence and the 3' UTRs from the respctive genome.
I am considering using miRanda as part of my pipeline (along with other target prediction tools).
However, since my set of species is rather evolutionarliy diverse (it icludes mammals, reptiles, ifsh amphbians, c.elegans and Drosophila), I wonder if the conservation filtering step of miRanda might not exclude possible targets for some of the species (especially the less annotated ones).
Is there some way to control the conservation threshold used by miRanda or the set of species against which conservation is estimated?
Alternatively, is there some other way to overcome this limitation?
Any suggestions will be appreciated.
Thanks in advance