ArticleGigaScience2016
RES-Scanner: a software package for genome-wide identification of RNA-editing sites.
Article in GigaScience, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Spatial transcriptomics reveals laminar and cell-type-specific A-to-I RNA editing signatures in the macaque cortex.Nature communications · 2026Article
- Epitranscriptomic Analysis of A-to-I RNA Editing and mInternational journal of molecular sciences · 2026Review
- A dynamic RNA editing landscape in porcine spleen highlights a post-transcriptional mechanism for immune maturation.Molecular genetics and genomics : MGG · 2026Article
- Article
- Landscape of A-I RNA editing in mouse, pig, macaque, and human brains.Nucleic acids research · 2025Article
- ncRNA Editing: Functional Characterization and Computational Resources.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Bioinformatics for Inosine: Tools and Approaches to Trace This Elusive RNA Modification.Genes · 2024Review
- Exploring functional conservation in silico: a new machine learning approach to RNA-editing.Briefings in bioinformatics · 2024Article
- Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases.Molecular therapy. Nucleic acids · 2024Review
- Harnessing ADAR-Mediated Site-Specific RNA Editing in Immune-Related Disease: Prediction and Therapeutic Implications.International journal of molecular sciences · 2023Review
- Article
- Benchmarking RNA Editing Detection Tools.Biotech (Basel (Switzerland)) · 2023Review
- Biological roles of A-to-I editing: implications in innate immunity, cell death, and cancer immunotherapy.Journal of experimental & clinical cancer research : CR · 2023Review
- Identification of exceptionally potent adenosine deaminases RNA editors from high body temperature organisms.PLoS genetics · 2023Article
- RNA Editing in Chloroplast: Advancements and Opportunities.Current issues in molecular biology · 2022Review
- Exploring the RNA Editing Events and Their Potential Regulatory Roles in Tea Plant (International journal of molecular sciences · 2022Article
- A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms.International journal of molecular sciences · 2022Article
- Breaking the limits - multichromosomal structure of an early eudicot Pulsatilla patens mitogenome reveals extensive RNA-editing, longest repeats and chloroplast derived regions among sequenced land plant mitogenomes.BMC plant biology · 2022Article
- ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts.Frontiers in cell and developmental biology · 2022Article
- A porcine brain-wide RNA editing landscape.Communications biology · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-throughput sequencing (HTS) provides a powerful solution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to distinguish RNA-editing sites from genetic variants and technical artifacts caused by sequencing or read-mapping errors.
resultsHere we present RES-Scanner, a flexible and efficient software package that detects and annotates RNA-editing sites using matching RNA-seq and DNA-seq data from the same individuals or samples. RES-Scanner allows the use of both raw HTS reads and pre-aligned reads in BAM format as inputs. When inputs are HTS reads, RES-Scanner can invoke the BWA mapper to align reads to the reference genome automatically. To rigorously identify potential false positives resulting from genetic variants, we have equipped RES-Scanner with sophisticated statistical models to infer the reliability of homozygous genotypes called from DNA-seq data. These models are applicable to samples from either single individuals or a pool of multiple individuals if the ploidy information is known. In addition, RES-Scanner implements statistical tests to distinguish genuine RNA-editing sites from sequencing errors, and provides a series of sophisticated filtering options to remove false positives resulting from mapping errors. Finally, RES-Scanner can improve the completeness and accuracy of editing site identification when the data of multiple samples are available.
conclusionRES-Scanner, as a software package written in the Perl programming language, provides a comprehensive solution that addresses read mapping, homozygous genotype calling, de novo RNA-editing site identification and annotation for any species with matching RNA-seq and DNA-seq data. The package is freely available.
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