DNAModAnnot: a R toolbox for DNA modification filtering and annotation.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
09 Sep 2021
09 Sep 2021
Historique:
received:
24
09
2020
revised:
17
12
2020
accepted:
13
01
2021
medline:
21
1
2021
pubmed:
21
1
2021
entrez:
20
1
2021
Statut:
ppublish
Résumé
Long-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. We 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. DNAModAnnot is distributed as a R package available via GitHub (https://github.com/AlexisHardy/DNAModAnnot). Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 33471071
pii: 6104827
doi: 10.1093/bioinformatics/btab032
pmc: PMC8428616
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2738-2740Subventions
Organisme : CNRS
Organisme : Fondation de la Recherche Médicale (Equipe FRM
ID : DEQ20160334868
Organisme : Agence Nationale de la Recherche
ID : ANR-18-CE12-0005-03
Organisme : GeT core facility
Organisme : France Génomique National infrastructure
Organisme : Agence Nationale pour la Recherche
ID : ANR-10-INBS-09
Organisme : GET-PACBIO
Organisme : FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press.
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