title: Annotating RNA motifs in sequences and alignments.
abstract: RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam.
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand paul.gardner@canterbury.ac.nz.
authors.forename: Paul P
authors.identifier: http://orcid.org/0000-0002-7808-1213
authors.initials: PP
authors.lastname: Gardner
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
authors.forename: Hisham
authors.initials: H
authors.lastname: Eldai
mesh_terms: D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D015233:Models, Statistical; D058977:Molecular Sequence Annotation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D012313:RNA