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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F26%3A0199415" target="_blank" >RIV/00216305:26220/26:0199415 - isvavai.cz</a>

Výsledek na webu

<a href="https://www.sciencedirect.com/science/article/pii/S2001037025004507" target="_blank" >https://www.sciencedirect.com/science/article/pii/S2001037025004507</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.csbj.2025.10.047" target="_blank" >10.1016/j.csbj.2025.10.047</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

DNA 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.

Název v anglickém jazyce

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

Popis výsledku anglicky

DNA 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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/GA23-05845S" target="_blank" >GA23-05845S: Určování infekčních hrozeb v reálném čase ze surových nanoporových signálů pomocí technik strojového učení</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Computational and Structural Biotechnology Journal

ISSN

—

e-ISSN

2001-0370

Svazek periodika

27

Číslo periodika v rámci svazku

October

Stát vydavatele periodika

SE - Švédské království

Počet stran výsledku

7

Strana od-do

4753-4759

Kód UT WoS článku

001612695400001

EID výsledku v databázi Scopus

2-s2.0-105020664171