title: In silico discovery and modeling of non-coding RNA structure in viruses.
abstract: 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.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.
authors.forename: Walter N
authors.initials: WN
authors.lastname: Moss
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA. Electronic address: joan.steitz@yale.edu.
authors.forename: Joan A
authors.initials: JA
authors.lastname: Steitz
mesh_terms: D003198:Computer Simulation; D004854:Herpesvirus 4, Human / Q000378:metabolism; D009980:Influenza A virus / Q000378:metabolism; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry* / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry*
chemical_list: D022661:RNA, Untranslated; D012367:RNA, Viral
keywords: RNA; RNA structure; Sequence analysis; Viruses; ncRNA; ncRNA prediction