you can try the mirDeep2

Dear Devrim

While mirDEEP suggested by Shan could be interesting, it might be restricted to seven or eight organisms.  And many a time, its peers in other organisms and relative crosschecking whether or not they are "unknown"  could be a daunting task. 

A few companies like Qiagen offers profiling pathway information focusing the  miRNAs and matured sequences.  You may have to use other tools, viz. http://bioinfo.au.tsinghua.edu.cn/mirnasvm/ to accurately predict the sequences and precursors.  

Hope this helps.

Prash 

You might also take a look at miRanalyzer. It uses a machine learning based approach to make predictions.

http://www.ncbi.nlm.nih.gov/pubmed/21515631

Thanks. 

Best wishes

Check out http://www.nature.com/natureevents/science/events/47533-microRNA_Analysis_Using_Next_Generation_Sequencing