ArticleBioinformatics (Oxford, England)2021
DNAModAnnot: a R toolbox for DNA modification filtering and annotation.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- A PIWI protein-dependent DNA N6-adenine methylation pathway inbioRxiv : the preprint server for biology · 2026Article
- Functions and mechanisms of eukaryotic RNA-guided programmed DNA elimination.Biochemical Society transactions · 2025Review
- Dynamic DNAGenome research · 2024Article
- Potential role of NiScience · 2023Article
- DNA Modification Patterns Filtering and Analysis Using DNAModAnnot.Methods in molecular biology (Clifton, N.J.) · 2023Article
- GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency inGenome research · 2022Article
- Broad domains of histone marks in the highly compactGenome research · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationLong-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect the integration of genomic annotation and comprehensive filtering when analyzing patterns of modified bases detected using Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) data. Here, we present DNA Modification Annotation (DNAModAnnot), a R package designed for the global analysis of DNA modification patterns using adapted filtering and visualization tools.
resultsWe tested our package using PacBio sequencing data to analyze patterns of the 6-methyladenine (6mA) in the ciliate Paramecium tetraurelia, in which high 6mA amounts were previously reported. We found P. tetraurelia 6mA genome-wide distribution to be similar to other ciliates. We also performed 5-methylcytosine (5mC) analysis in human lymphoblastoid cells using ONT data and confirmed previously known patterns of 5mC. DNAModAnnot provides a toolbox for the genome-wide analysis of different DNA modifications using PacBio and ONT long-read sequencing data. AVAILABILITY AND IMPLEMENTATION: DNAModAnnot is distributed as a R package available via GitHub (https://github.com/AlexisHardy/DNAModAnnot). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.