Single-sequence submissions to PREP-Mt or PREP-Cp

Input

PREP-Mt and PREP-Cp require that the user provides information for five parameters. A brief description of these parameters is given below.

  1. Enter a protein-coding DNA sequence.
     
  2. Choose the codon position of the first nucleotide.
     
  3. Enter a name for the input DNA sequence.
     
  4. Which gene is it?
     
  5. Provide a minimum cutoff value (C).
     

Output

PREP-Mt and PREP-Cp will return information regarding the position, effect, and score of each predicted edit site. Downloadable files containing the prediction results and the predicted sequences after editing are also provided in the "Download Data Files" section of the output. A brief description of the output is given below.

  1. Position
     
  2. Effect
     
  3. Score
     
  4. Download data files
     

Batch submissions to PREP-Mt or PREP-Cp

The batch submission option for PREP-Mt and PREP-Cp allows the user to obtain predictions for multiple sequences at once. You will be required to submit a tab-delimited text file containing all the necessary information (format described below). Output is similar to the single-sequence mode, except that the downloadable data files for all sequences are combined and stored as compressed archives.

Tab-delimited text file

The input file for batch mode is a tab-delimited text file that contains the following five parameters separated by a tab, with each sequence to be tested on a separate line:

  1. A sequence name (must be unique and less than 30 characters).
  2. The gene name (must be identical to one of the gene names listed in single-sequence mode.)
  3. The codon position of the first nucleotide (must be 1, 2, or 3).
  4. The cutoff value (must be between 0 and 1).
  5. The DNA sequence (must be IUPAC symbols only and less than 10 kb in length).

Downloadable data archives

The downloadable data files for all examined sequences are compressed and archived together in two formats: a gzipped tar arhive (.tar.gz) and a zipped archive (.zip). Choose the format that is best for your operating system.


Alignment submissions to PREP-Aln

PREP-Aln allows the user to use the PREP methodology to predict sites of RNA editing in a custom alignment containing a mix of DNA and RNA sequences. The RNA sequences will be translated to form the alignment that guides prediction in the DNA sequences. Output is similar to the other methods. This feature is provided to allow the user to predict edit sites in any alignment of interest. Using PREP-Aln, the user could take advantage of new or unpublished editing data or to optimize prediction performance.

To use PREP-Aln, the user must provide a codon-based nucleotide alignment in FASTA format, consisting of protein-coding sequences aligned by codon. Gaps must be placed between codons and gap lengths must be in multiples of three. To ensure propor formatting, placement of gaps in the codon alignment should be guided by an alignment of the translated protein sequences. Online resources, such as PAL2NAL and RevTrans are available to help generate codon-based alignments.

The alignment submitted to PREP-Aln must contain at least one RNA sequence and and any number of DNA sequences. More RNA sequences will likely improve performance. To ensure recognition by PREP-Aln, all RNA sequences in the alignment must be flagged by adding "_RNA" to the end of their definition lines. Please use this sample alignment as a guide for proper formatting.


References

Mower, J. P. (2005). PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinformatics, 6:96. [Article]

Mower, J. P. (2009). The PREP Suite: Predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucl. Acids Res., 37:W253-W259. [Article]