SPRINT: an SNP-free Toolkit for Identifying RNA Editing Sites

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2017 Oct 17

PMID 29036410

Citations 53

Authors

Feng Zhang

Yulan Lu

Sijia Yan

Qinghe Xing

Weidong Tian

Affiliations

Soon will be listed here.

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 have applied SPRINT to investigate RNA editing across tissues and species, and also in the development of mouse embryonic central nervous system. A web resource (http://sprint.tianlab.cn) of RESs identified by SPRINT has been constructed.

Availability And Implementation: The software and related data are available at http://sprint.tianlab.cn.

Contact: weidong.tian@fudan.edu.cn.

Supplementary Information: Supplementary data are available at Bioinformatics online.

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