Principles and limitations of computational microRNA gene and target finding

In 2001 there were four PubMed entries matching the word "microRNA" (miRNA). Interestingly, this number has now far exceeded 1300 and is still rapidly increasing. This more than anything demonstrates the extreme attention this field has had within a short period of time. With the large amounts of sequence data being generated, the need for analysis by computational approaches is obvious. Here, we review the general principles used in computational gene and target finding, and discuss the strengths and weaknesses of the methods. Several methods rely on detection of evolutionary conserved candidates, but recent methods have challenged this paradigm by simultaneously searching for the gene and the corresponding target(s). Whereas the early methods made predictions based on sets of hand-derived rules from precursor-miRNA structure or observed target-miRNA interactions, recent methods apply machine learning techniques. Even though these methods are already powerful, the amount of data they rely on is still limited. Since it is evident that data are continuously being generated, it must be anticipated that these methods will further improve their performance.