Identification of viral microRNAs.

Given the important function of microRNAs (miRNAs) in the control of gene expression, it is not surprising to find that some viruses encode their own miRNAs. Although the function of the overwhelming majority of these miRNAs remains unknown, at least some of them are expected to play crucial roles in the viral life cycle, and hence there is great interest in identifying novel viral miRNAs. The majority of currently known viral (and host) miRNAs have been identified by cloning of small RNAs, but, due to their small size, viral genomes are especially amenable to alternative methods based on the computational prediction of miRNA candidates. Here, we provide a detailed protocol on how to use computational prediction methods in conjunction with high-throughput microarray analysis to detect miRNAs in viral genomes.