Bacterial phenotype prediction based on methylation site profiles

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F23%3APU148965" target="_blank" >RIV/00216305:26220/23:PU148965 - isvavai.cz</a>

Výsledek na webu

<a href="https://ieeexplore.ieee.org/document/10264900" target="_blank" >https://ieeexplore.ieee.org/document/10264900</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/CIBCB56990.2023.10264900" target="_blank" >10.1109/CIBCB56990.2023.10264900</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Bacterial phenotype prediction based on methylation site profiles

Popis výsledku v původním jazyce

Methylated site mapping in the DNA sequences plays a key role in understanding the physiology and pathology of cells and organisms. Thanks to third-generation DNA sequencers, these epigenetic modifications can be detected already when reading genetic information. Therefore, not only genotypic classification but also phenotypic specifications can be determined based on a single sequencing run. However, for phenotyping purposes, there is still a lack of effective standardized tools to design uniform classification schemes for different laboratories. Here, we present a simple tool for comparing DNA methylation site profiles, utilizing sequencing reads mapping to the reference genome similar to core genome analysis in bacterial genotyping. The proposed pipeline maps sequence reads with marked positions of methylated bases to a single representative reference. Thus the output consists of the uniformly aligned methylated site positions in a set of bacterial genomes. This allows for the evaluation of common methylated sites across all genomes, i.e. ,,core methylome”, as well as unique methylated sites in gene and intergenic regions. Thus, determining the sequence type can be further refined by predicting bacterial behaviour such as antibiotic resistance or virulence.

Název v anglickém jazyce

Bacterial phenotype prediction based on methylation site profiles

Popis výsledku anglicky

Methylated site mapping in the DNA sequences plays a key role in understanding the physiology and pathology of cells and organisms. Thanks to third-generation DNA sequencers, these epigenetic modifications can be detected already when reading genetic information. Therefore, not only genotypic classification but also phenotypic specifications can be determined based on a single sequencing run. However, for phenotyping purposes, there is still a lack of effective standardized tools to design uniform classification schemes for different laboratories. Here, we present a simple tool for comparing DNA methylation site profiles, utilizing sequencing reads mapping to the reference genome similar to core genome analysis in bacterial genotyping. The proposed pipeline maps sequence reads with marked positions of methylated bases to a single representative reference. Thus the output consists of the uniformly aligned methylated site positions in a set of bacterial genomes. This allows for the evaluation of common methylated sites across all genomes, i.e. ,,core methylome”, as well as unique methylated sites in gene and intergenic regions. Thus, determining the sequence type can be further refined by predicting bacterial behaviour such as antibiotic resistance or virulence.

Druh

D - Stať ve sborníku

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

2023

Kód důvěrnosti údajů

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

Název statě ve sborníku

2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)

ISBN

979-8-3503-1017-7

ISSN

—

e-ISSN

—

Počet stran výsledku

6

Strana od-do

1-6

Název nakladatele

IEEE

Místo vydání

neuveden

Místo konání akce

Eindhoven

Datum konání akce

29. 8. 2023

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

001090563700005