In silico discovery and modeling of non-coding RNA structure in viruses

• A review of methods for the in silico discovery and modeling of non-coding RNA structure in viruses is presented.
• Methods based on free energy minimization are discussed.
• Methods based on sequence analysis are discussed.
• Examples are given from previous work on influenza A and Epstein–Barr virus.
• A brief protocol is presented using influenza A segment 5 as an example.

This review covers several computational methods for discovering structured non-coding RNAs in viruses and modeling their putative secondary structures. Here we will use examples from two target viruses to highlight these approaches: influenza A virus—a relatively small, segmented RNA virus; and Epstein–Barr virus—a relatively large DNA virus with a complex transcriptome. Each system has unique challenges to overcome and unique characteristics to exploit. From these particular cases, generically useful approaches can be derived for the study of additional viral targets.