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Annotating RNA motifs in sequences and alignments

View ORCID ProfilePaul P. Gardner, View ORCID ProfileHisham Eldai
doi: https://doi.org/10.1101/011197
Paul P. Gardner
1School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
2Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
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  • For correspondence: paul.gardner@canterbury.ac.nz
Hisham Eldai
1School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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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 characterise RNA motifs, which are the central building blocks of RNA structure. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterised RNAs. Moreover, we introduce a new profile-based database of RNA motifs - RMfam - and illustrate its application for investigating the evolution and functional characterisation of RNA.

All the data and scripts associated with this work is available from: https://github.com/ppgardne/RMfam

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 06, 2014.
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Annotating RNA motifs in sequences and alignments
Paul P. Gardner, Hisham Eldai
bioRxiv 011197; doi: https://doi.org/10.1101/011197
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Annotating RNA motifs in sequences and alignments
Paul P. Gardner, Hisham Eldai
bioRxiv 011197; doi: https://doi.org/10.1101/011197

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