RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs
- Jeremy Widmann1,
- Jesse Stombaugh1,
- Daniel McDonald2,
- Jana Chocholousova3,
- Paul Gardner4,
- Matthew K. Iyer5,
- Zongzhi Liu6,
- Catherine A. Lozupone1,
- John Quinn7,
- Sandra Smit8,
- Shandy Wikman9,
- Jesse R.R. Zaneveld10 and
- Rob Knight1,11,12
- 1Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
- 2Biofrontiers Institute, University of Colorado at Boulder, Boulder, Colorado 80309, USA
- 3Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
- 4School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- 5Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
- 6Department of Pathology Informatics, School of Medicine, Yale University, New Haven, Connecticut 06510, USA
- 7Thermo Fisher Scientific, Lafayette, Colorado 80026, USA
- 8Laboratory of Bioinformatics, Wageningen University, 6700 AN Wageningen, The Netherlands
- 9Hägersten 12930, Sweden
- 10Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
- 11Howard Hughes Medical Institute, Boulder, Colorado 80309, USA
Abstract
Automated RNA alignment algorithms often fail to recapture the essential conserved sites that are critical for function. To assist in the refinement of these algorithms, we manually curated a set of 148 alignments with a total of 9600 unique sequences, in which each alignment was backed by at least one crystal or NMR structure. These alignments included both naturally and artificially selected molecules. We used principles of isostericity to improve the alignments from an average of 83%–94% isosteric base pairs. We expect that this alignment collection will assist in a wide range of benchmarking efforts and provide new insight into evolutionary principles governing change in RNA structural motifs. The improved alignments have been contributed to the Rfam database.
Keywords
Footnotes
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↵12 Corresponding author
E-mail rob.knight{at}colorado.edu
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.032052.111.
- Received December 30, 2011.
- Accepted May 2, 2012.
- Copyright © 2012 RNA Society
Freely available online through the RNA Open Access option.
