aPPRove: A HMM-based Method for Accurate Prediction of RNA and Pentatricopeptide Repeat Protein Binding



As the name ‚Äúpentatricopeptide repeat‚ÄĚ describes, the PPR class of RNA-binding proteins are classified by the existence of tandem degenerate PPR motif sequences which have approximately 35 amino acids, and any number of repeats. The repeated motif sequences interact with an RNA binding site.

aPPRove takes as input a PPR protein (primary structure), one or more RNA transcripts or binding footprints, and outputs the binding sites that have highest statistical significance, and how the nucleic acids in the RNA aligned to the amino acid pairs (defined by positions 6 and 1') in the PPR sequence for each binding. The statistical significance is based on the significance of the alignment in comparison to random alignments of the PPR to a database of transcripts. aPPRove harnesses the code Barkan et al and implements a tailored hidden Markov algorithm to determine a score of each possible binding. aPPRove can be used to locate how and where a PPR protein belonging to the PLS subfamily.

To Run aPPRove From This Site:

  • Click the Run aPPRove tab located at the top of this page
  • Enter and confirm your email adresses in the text feilds. The results will be emailed to this address
  • Upload a protein and target RNA sequence(s). Both should be fasta files
  • You have the option of uploading a database file in the form of a fasta file. aPPRove will report a p-value of each alignment to the target sequence using a distribution formed by aligning the PPR protein against this database
  • Enter the number of optimal results to be returned by aPPRove in the coresponding text box. This should be in the form of an integer
  • Click the Submit button
  • Your results will be emailed to you

Results include:

  • A list of aPPRoves w hits along the transcript which include their score and adjusted p-value.
  • A list of aPPRoves w hits among all provided transcripts which include their score and adjusted p-value.
  • A pdf displaying the distribution of all normalized scores of randomn alignments to the database (default database is transcripts from the Arabadopsis thailiana chloroplast).
  • A list of all alignments to the data base that scored higher than the alignment to the target.
Fujii S., Bond, C.D., and Small, I.D (2011). The evolution of RNA editing pentatricopeptide genes. NewPhytol. 191: 37-47

Contributers:

Contact Us:

Please email us at: thomas.harrison@cs.colostate.edu

Please contact us if more known PPR-RNA proteins are known and available for use so we can further update our model.

Download:

The aPPRove software can also be downloaded from this link. Data used in the manuscript can be downlaoded from this link.

Software:

aPPRove is distributed under the terms of the GNU General Public License