{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T00:30:15Z","timestamp":1767918615855,"version":"3.49.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,1,20]],"date-time":"2021-01-20T00:00:00Z","timestamp":1611100800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012681","name":"CNRS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012681","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002915","name":"Fondation de la Recherche M\u00e9dicale","doi-asserted-by":"crossref","award":["Equipe FRM DEQ20160334868"],"award-info":[{"award-number":["Equipe FRM DEQ20160334868"]}],"id":[{"id":"10.13039\/501100002915","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-18-CE12-0005-03; ANR-19-CE12-0015-01"],"award-info":[{"award-number":["ANR-18-CE12-0005-03; ANR-19-CE12-0015-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DNAModAnnot is distributed as a R package available via GitHub (https:\/\/github.com\/AlexisHardy\/DNAModAnnot).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab032","type":"journal-article","created":{"date-parts":[[2021,1,14]],"date-time":"2021-01-14T21:53:49Z","timestamp":1610661229000},"page":"2738-2740","source":"Crossref","is-referenced-by-count":9,"title":["DNAModAnnot: a R toolbox for DNA modification filtering and annotation"],"prefix":"10.1093","volume":"37","author":[{"given":"Alexis","family":"Hardy","sequence":"first","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS, Institut Jacques Monod , F-75006 Paris, France"}]},{"given":"M\u00e9lody","family":"Matelot","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS, Institut Jacques Monod , F-75006 Paris, France"}]},{"given":"Amandine","family":"Touzeau","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS, Institut Jacques Monod , F-75006 Paris, France"}]},{"given":"Christophe","family":"Klopp","sequence":"additional","affiliation":[{"name":"Plateforme bioinformatique Genotoul, UR875 Math\u00e9matique et Informatique Appliqu\u00e9e de Toulouse, INRA , 31326 Castanet-Tolosan, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2529-7958","authenticated-orcid":false,"given":"C\u00e9line","family":"Lopez-Roques","sequence":"additional","affiliation":[{"name":"INRAe, US 1426, GeT-PlaGe, Genotoul , 31326 Castanet-Tolosan, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8913-8799","authenticated-orcid":false,"given":"Sandra","family":"Duharcourt","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS, Institut Jacques Monod , F-75006 Paris, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3090-3142","authenticated-orcid":false,"given":"Matthieu","family":"Defrance","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Libre de Bruxelles, Interuniversity Institute of Bioinformatics in Brussels (IB2) , Brussels 1050, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2021,1,20]]},"reference":[{"key":"2023051609162319600_btab032-B1","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13059-020-1935-5","article-title":"Opportunities and challenges in long-read sequencing data analysis","volume":"21","author":"Amarasinghe","year":"2020","journal-title":"Genome Biol"},{"key":"2023051609162319600_btab032-B2","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1016\/j.cell.2019.04.028","article-title":"Identification of a DNA N6-adenine methyltransferase complex and its impact on chromatin organization","volume":"177","author":"Beh","year":"2019","journal-title":"Cell"},{"key":"2023051609162319600_btab032-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0005-2787(74)90194-4","article-title":"Methylated bases in DNA from Paramecium aurelia","volume":"374","author":"Cummings","year":"1974","journal-title":"Biochim. 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