Nucleic Acids Research Advance Access originally published online on May 11, 2009
Nucleic Acids Research 2009 37(Web Server issue):W253-W259; doi:10.1093/nar/gkp337
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W253-W259
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments
1Center for Plant Science Innovation and 2Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA
*To whom correspondence should be addressed. Tel: +1 402 472 2130; Fax: +1 402 472 3139; Email: jmower2{at}unl.edu
Received February 17, 2009. Revised April 11, 2009. Accepted April 21, 2009.
RNA editing alters plant mitochondrial and chloroplast transcripts by converting specific cytidines to uridines, which usually results in a change in the amino acid sequence of the translated protein. Systematic studies have experimentally identified sites of RNA editing in organellar transcriptomes from several species, but these analyses have not kept pace with rate of genome sequencing. The PREP (predictive RNA editors for plants) suite was developed to computationally predict sites of RNA editing based on the well-known principle that editing in plant organelles increases the conservation of proteins across species. The PREP suite provides predictive RNA editors for plant mitochondrial genes (PREP-Mt), for chloroplast genes (PREP-Cp), and for alignments submitted by the user (PREP-Aln). These servers require minimal input, are very fast, and are highly accurate on all seed plants examined to date. PREP-Mt has proved useful in several research studies and the newly developed PREP-Cp and PREP-Aln servers should be of further assistance for analyses that require knowledge of the location of sites of RNA editing. The PREP suite is freely available at http://prep.unl.edu/.