An Automated Approach to Identify RNA Editing Sites |Biomedgrid

RNA-editing is one type of post transcription modifications on RNA sequences. To detect RNA-editing, one method is to compare mature mRNA (or cDNA) with the sequences in the coding region. In most existing studies, the coding region sequences were extracted from the reference genome, and therefore SNPs are also detected during this comparison. In this study, both the coding region sequences and the mature mRNAs or cDNAs were from the same genome. Therefore, the detected variations from the mature mRNAs and the coding regions would be either RNA-editing sites or sequencing errors. We developed an automated and computational approach to identify RNA editing sites and the clusters with highly frequent RNA-editing sites. The results of our computational approach provided a candidate list of genes that are most likely to contain the coding regions that represent RNA editing sites. The results also showed that most of the “A-to-G” editing sites located in the 3' regions, followed by transcript and exonic regions. Moreover, we have provided a visualization of the editing sites within genes and chromosomes. Since the experimental clinical studies to identify the RNA editing sites are very resource intensive in terms of cost, time, and efforts, so our results will be used to define the initial candidate list of genes that should be experimentally tested.