Hi Fulvio

There are many applications for denovo miRNA prediction. I personally used with success this one from the swiss Biozentrum. It is called MiRAbela:

http://www.mirz.unibas.ch/cgi/pred_miRNA_genes.cgi

You have many other applications for the same purpose compiled in my humble site with tools related with miRNA research.

https://sites.google.com/site/mirnatools/mirna-prediction

Hope it helps. Good luck. Cheers

Paco

A similar question has been asked here:

https://www.researchgate.net/post/How_to_predict_miRNA_using_bioinformatics_tools

But in respect to your question only this site may be of additional interest:

http://www.exiqon.com/microrna-target-prediction

Also, maybe our recent review can be of interest as well: https://www.researchgate.net/publication/232536328_Computational_methods_for_ab_initio_detection_of_microRNAs

Article Computational methods for ab initio detection of microRNAs

Hi Paco, thanks for your answer...MIRAbela works only with sequence of 1kb..so I have to scan 30Kb...piece by piece so :) I'll give it a try anyway...I've also checked your "humble site" (nice, by the way, well done), but miRNAFinder's link seems broken..and I also tried to google it, but with no results...do you have any suggestion?