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DNAModAnnot: a R toolbox for DNA modification filtering and annotation.

Alexis Hardy¹, Mélody Matelot¹, Amandine Touzeau¹

¹Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France.

Bioinformatics (Oxford, England)

|January 20, 2021

Summary

This summary is machine-generated.

DNAModAnnot is a new R package for analyzing DNA modifications from long-read sequencing data. It integrates genomic annotation and filtering for PacBio and ONT data, enabling genome-wide DNA modification pattern analysis.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Long-read sequencing technologies enable nucleotide-resolution, genome-wide DNA modification detection.
Existing software lacks genomic annotation and comprehensive filtering for PacBio and ONT data analysis.
DNA modifications play crucial roles in gene regulation and cellular processes.

Purpose of the Study:

To introduce DNAModAnnot, an R package for global DNA modification pattern analysis.
To provide integrated genomic annotation and filtering tools for long-read sequencing data.
To facilitate the study of DNA modification patterns using PacBio and ONT technologies.

Main Methods:

DNAModAnnot is implemented as an R package, available on GitHub.
The package incorporates adapted filtering and visualization tools for DNA modification analysis.
It supports the analysis of various DNA modifications, including 6-methyladenine (6mA) and 5-methylcytosine (5mC).

Main Results:

DNAModAnnot was validated using PacBio data to analyze 6mA patterns in *Paramecium tetraurelia*.
Genome-wide 6mA distribution in *P. tetraurelia* was found to be consistent with other ciliates.
5-methylcytosine (5mC) patterns in human cells were confirmed using ONT data.

Conclusions:

DNAModAnnot offers a comprehensive toolbox for genome-wide DNA modification analysis.
The package effectively utilizes long-read sequencing data from PacBio and ONT.
It enhances the analysis of DNA modification patterns by integrating annotation and filtering capabilities.