I know this sort of question has been posted previously here , but I was hoping still if anyone here could direct me to an actual paper where there is a good suggestion for a cutoff value for the match score and the free energy for a particular miRNA-target pairing entry in miRanda. I am using the software (miRanda) locally on unix on my dataset and have generated thousands of hits with a strict match on the seed region (--strict option in miRanda)

I have referred to the Plos Biology and Genome Biology papers (2004 and 2003 respectively) for referral to a cut off but really have not found a distinct value. I will check again, in case I missed out on it. But since the forum has so many experienced researchers- I was hoping for any feedback from your end ( or any article reference) for a cut off value for miRanda in the Match score and the free energy values.

Thanks and regards !