GIREMI Identify RNA editing sites


GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.

GIREMI calculates the mutual information (MI) of the mismatch pairs identified in the RNA-seq reads to distinguish RNA editing sites and SNPs. It also trains a generalized linear model (GLM) to achieve enhanced predictive power, which makes use of sequence bias information and the difference between the mismatch ratio of the unknown single nucleotide variants (SNVs) and the estimated allelic ratio of the gene.


  1. Genome sequence–independent identification of RNA editing sites
    Qing Zhang & Xinshu Xiao, 2015 - Nature Methods
    Cited by Zhang Q, Xiao X. Genome sequence-independent identification of RNA editing sites. Nat Methods. 2015 Apr;12(4):347-50. doi: 10.1038/nmeth.3314. Epub 2015 Mar 2. PubMed PMID: 25730491; PubMed Central PMCID: PMC4382388. (Google Schoolar as of September 5, 2017)


  1. Qing Zhang

    University of California, Department of Integrative Biology and Physiology, United States of America

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dot*** (August 15, 2017)
Tool TypeApplication
CategoryRNA editing
TechnologiesC, Perl, R
User InterfaceTerminal Command Line
Input DataBAM
Download Count0
Submitted Byli man