SPRINT: an SNP-free toolkit for identifying RNA editing sites.

ABSTRACT:

Motivation

RNA editing generates post-transcriptional sequence alterations. Detection of RNA editing sites (RESs) typically requires the filtering of SNVs called from RNA-seq data using an SNP database, an obstacle that is difficult to overcome for most organisms.

Results

Here, we present a novel method named SPRINT that identifies RESs without the need to filter out SNPs. SPRINT also integrates the detection of hyper RESs from remapped reads, and has been fully automated to any RNA-seq data with reference genome sequence available. We have rigorously validated SPRINT's effectiveness in detecting RESs using RNA-seq data of samples in which genes encoding RNA editing enzymes are knock down or over-expressed, and have also demonstrated its superiority over current methods. We

SUBMITTER: Zhang F 

PROVIDER: S-EPMC5870768 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature