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REDO

Posted on by Robin Ding Leave a comment Bio-Informatics, Molecular Science

REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in multiple samples simultaneously and identify differential proportion of RNA editing events in different samples. Moreover, the genome variation can be easily removed by a subprogram fish.pl in our package.

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Website https://redo.sourceforge.io
Tags
License GNU General Public License version 3.0 (GPLv3)
Platform Linux Windows
Features
  • The false positive are filtered by rule-depended filters and statistics filters
  • The detailed annotations are provided, including gene name, nucleotide and amino acid position in gene, codon phase, ref and editing alleles, ref and editing codons, ref and editing amino acids, editing proportion, gene function, etc.
  • Useful statistics are also provided by REDO, such as the statistics for RNA editing types, hydrophobic/hydrophilic changes, silent/non-silent changes and codon phases of editing sites.
  • For illustrating the attributes of RNA editing sites, 16 figures are produced using R program for each sample.
  • REDO can detect RNA editing events in multiple samples simultaneously.
  • The differential proportion of RNA editing events in multiple samples can be identified.
  • The subprogram can be used to process the REDO result tables easily and quickly.