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

Abstract

MotivationRNA 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.ResultsHere, 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 implementationThe software and related data are available at http://sprint.tianlab.cn.Supplementary information Supplementary data are available at Bioinformatics online.

Comparative Analysis of the Transcriptional Response of Tolerant and Sensitive Wheat Genotypes to Drought Stress in Field Conditions

“…To identify the RNA editing sites of these two wheat varieties between irrigated and drought-stressed, all the clean reads of RNA-seq were mapped to the wheat genome IWGSC RefSeq v1.0 using SPRINT (SnP-free RNA editing IdeNtification Toolkit) software with default parameters [46]. To avoid any errors, the independencies mapping software BWA (http://biobwa.sourceforge.net) [47] and SNP nomenclature tools Samtools (http://www.htslib.org) [48] were integrated to identify the SNP between RNA reads and reference genomic DNA.…”

A comprehensive study on chloroplast RNA editing by performing a broad-spectrum RNA-seq analysis

“…Thus, we used the preliminary output from variant calling software to identify RNA editing sites. For each plant, based on the SNP-calling results (in "VCF" format) and genome annotation les (in "tbl" format), the RNA editing sites were identi ed under default parameter values by using the REDO tool [21]. features of RNA editing sites, which are RNA editing types, alt proportion, amino acids change, codon phase, and hydrophobic/hydrophilic change.…”

“…Indeed, the number of complete plant organellar genomes and related transcriptome data have considerably grown in the last decade, and tens of thousands of editing sites have been identi ed in more and more plants [18,19]. However, this strategy is also a challenging task due to its accuracy of mapping the RNA-seq reads against genomic sequence, hence, so different bioinformatic strategies have been introduced to improve the detection of RNA editing sites [20][21][22].…”

RNA Editing Signatures Predict Response to Immunotherapies in Melanoma Patients

“…Sprint was used on the resulting BAM alignment files to identify RNA editing sites de novo. 8 The changesammapq.py script from Sprint was used to convert the BAM files to the correct format for Sprint 8 . The sprint_from_bam.py script was used to identify regular RNA editing sites from the resulting BAM file using the GRCh8 p12 genome release 31 6 and Sprint-provided hg38 repeat annotations.…”