title: RNAs everywhere: genome-wide annotation of structured RNAs.
abstract: Starting with the discovery of microRNAs and the advent of genome-wide transcriptomics, non-protein-coding transcripts have moved from a fringe topic to a central field research in molecular biology. In this contribution we review the state of the art of "computational RNomics", i.e., the bioinformatics approaches to genome-wide RNA annotation. Instead of rehashing results from recently published surveys in detail, we focus here on the open problem in the field, namely (functional) annotation of the plethora of putative RNAs. A series of exploratory studies are used to provide non-trivial examples for the discussion of some of the difficulties.
authors.affiliation: Bioinformatics Group, Department of Computer Science, University of Freiburg, D-79110 Freiburg, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.forename: Stephan H
authors.initials: SH
authors.lastname: Bernhart
authors.forename: Christoph
authors.initials: C
authors.lastname: Flamm
authors.forename: Claudia
authors.initials: C
authors.lastname: Fried
authors.forename: Guido
authors.initials: G
authors.lastname: Fritzsch
authors.forename: Jörg
authors.initials: J
authors.lastname: Hackermüller
authors.forename: Jana
authors.initials: J
authors.lastname: Hertel
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
authors.forename: Kristin
authors.initials: K
authors.lastname: Missal
authors.forename: Axel
authors.initials: A
authors.lastname: Mosig
authors.forename: Sonja J
authors.initials: SJ
authors.lastname: Prohaska
authors.forename: Dominic
authors.initials: D
authors.lastname: Rose
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Andrea
authors.initials: A
authors.lastname: Tanzer
authors.forename: Stefan
authors.initials: S
authors.lastname: Washietl
authors.forename: Sebastian
authors.initials: S
authors.lastname: Will
mesh_terms: D005075:Biological Evolution; D019295:Computational Biology; D016678:Genome; D012313:RNA / Q000737:chemistry / Q000145:classification* / Q000235:genetics*
chemical_list: D012313:RNA