MethylomeMiner: A novel tool for high-resolution analysis of bacterial methylation patterns from nanopore sequencing

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dc.contributor.authorJakubíčková, Markétacs
dc.contributor.authorŠabatová, Kateřinacs
dc.contributor.authorZbudilová, Michaelacs
dc.contributor.authorBezdíček, Matějcs
dc.contributor.authorLengerová, Martinacs
dc.contributor.authorVítková, Helenacs
dc.coverage.issueOctobercs
dc.coverage.volume27cs
dc.date.issued2025-10-24cs
dc.description.abstractDNA methylation plays a key role in gene regulation, genome stability, bacterial adaptation, and many other essential cellular processes. Thanks to nanopore sequencing technology, it is now possible to detect these modifications during sequencing without any prior chemical treatment. However, methylation data processing and their interpretation in a biological context remain challenging as there are no convenient and easy-to-use tools available for this purpose. Therefore, here, we present a simple Python-based tool, MethylomeMiner, to process methylation calls from nanopore sequencing. The tool allows high-confidence methylation sites to be selected based on coverage and methylation rate and assigned to coding or non-coding regions using genome annotation. In addition, the tool supports population-level analysis using pangenome data to compare methylation patterns across multiple bacterial genomes. Altogether, MethylomeMiner provides a straightforward and reproducible workflow that can be easily integrated into existing analyses and helps uncover the functional roles of DNA methylation in bacterial genomes.en
dc.description.abstractDNA methylation plays a key role in gene regulation, genome stability, bacterial adaptation, and many other essential cellular processes. Thanks to nanopore sequencing technology, it is now possible to detect these modifications during sequencing without any prior chemical treatment. However, methylation data processing and their interpretation in a biological context remain challenging as there are no convenient and easy-to-use tools available for this purpose. Therefore, here, we present a simple Python-based tool, MethylomeMiner, to process methylation calls from nanopore sequencing. The tool allows high-confidence methylation sites to be selected based on coverage and methylation rate and assigned to coding or non-coding regions using genome annotation. In addition, the tool supports population-level analysis using pangenome data to compare methylation patterns across multiple bacterial genomes. Altogether, MethylomeMiner provides a straightforward and reproducible workflow that can be easily integrated into existing analyses and helps uncover the functional roles of DNA methylation in bacterial genomes.en
dc.formattextcs
dc.format.extent4753-4759cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationComputational and Structural Biotechnology Journal. 2025, vol. 27, issue October, p. 4753-4759.en
dc.identifier.doi10.1016/j.csbj.2025.10.047cs
dc.identifier.issn2001-0370cs
dc.identifier.orcid0000-0002-0205-6935cs
dc.identifier.orcid0000-0001-5143-9521cs
dc.identifier.orcid0000-0002-5833-8325cs
dc.identifier.orcid0000-0001-8739-9998cs
dc.identifier.orcid0000-0003-4562-2746cs
dc.identifier.other199415cs
dc.identifier.researcheridR-3181-2018cs
dc.identifier.researcheridAAC-2736-2019cs
dc.identifier.researcheridD-5194-2014cs
dc.identifier.scopus57202469794cs
dc.identifier.scopus57205673155cs
dc.identifier.scopus36521691000cs
dc.identifier.urihttp://hdl.handle.net/11012/255625
dc.language.isoencs
dc.relation.ispartofComputational and Structural Biotechnology Journalcs
dc.relation.urihttps://www.sciencedirect.com/science/article/pii/S2001037025004507cs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/2001-0370/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectMethylomeen
dc.subjectEpigeneticsen
dc.subjectBedMethyl tablesen
dc.subjectPangenomeen
dc.subjectPython packageen
dc.subjectMethylome
dc.subjectEpigenetics
dc.subjectBedMethyl tables
dc.subjectPangenome
dc.subjectPython package
dc.titleMethylomeMiner: A novel tool for high-resolution analysis of bacterial methylation patterns from nanopore sequencingen
dc.title.alternativeMethylomeMiner: A novel tool for high-resolution analysis of bacterial methylation patterns from nanopore sequencingen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
eprints.grantNumberinfo:eu-repo/grantAgreement/GA0/GA/GA23-05845Scs
sync.item.dbidVAV-199415en
sync.item.dbtypeVAVen
sync.item.insts2025.11.20 15:49:19en
sync.item.modts2025.11.20 15:23:04en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
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