Detail publikace

Rapid bacterial species delineation based on parameters derived from genome numerical representations

MADĚRÁNKOVÁ, D. JUGAS, R. SEDLÁŘ, K. VÍTEK, M. ŠKUTKOVÁ, H.

Originální název

Rapid bacterial species delineation based on parameters derived from genome numerical representations

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální abstrakt

Species delineation based on bacterial genomes is an essential part of the research of prokaryotes. In silico genome-to-genome comparison methods are computationally demanding, but much less tedious and error prone than the wet-lab methods. In this paper, we present a novel method for the delineation of bacterial genomes based on genomic signal processing. The proposed method uses numerical representations of whole bacterial genomes, phase signal and cumulated phase signal, from which four parameters are derived for each genome. The parameters characterize a genome and their calculation is independent of the other genomes comprising a delineation dataset. The delineation itself is processed as a calculation of the parameters’ average similarity. The method was statistically verified on 1,826 bacterial genomes. A similarity threshold of 96% was set based on the receiver operating characteristic curve that featured sensitivity of 99.78% and specificity of 97.25%. Additionally, comparative analysis on another 33 bacterial genomes was conducted using standard delineation tools as these tools were not able to process the dataset of 1,826 genomes using desktop computer. The proposed method achieved comparable or better delineation results in comparison with the standard tools. Besides the excellent delineation results, another great advantage of the method is its small computational demands, which enables the delineation of thousands of genomes on a desktop computer. The calculation of the parameters takes tens of minutes for thousands of genomes. Moreover, they can be calculated in advance by creating a database, meaning the delineation itself is then completed in a matter of seconds.

Klíčová slova

bacterial genome, species delineation, comparative genomics, numerical representation, genomic signal processing

Autoři

MADĚRÁNKOVÁ, D.; JUGAS, R.; SEDLÁŘ, K.; VÍTEK, M.; ŠKUTKOVÁ, H.

Vydáno

9. 1. 2019

Nakladatel

Elsevier

ISSN

2001-0370

Periodikum

Computational and Structural Biotechnology Journal

Ročník

17

Číslo

1

Stát

Švédské království

Strany od

118

Strany do

126

Strany počet

9

URL

http://www.sciencedirect.com/science/article/pii/S2001037018301223

BibTex

@article{BUT152123,
  author="Denisa {Maděránková} and Robin {Jugas} and Karel {Sedlář} and Martin {Vítek} and Helena {Vítková}",
  title="Rapid bacterial species delineation based on parameters derived from genome numerical representations",
  journal="Computational and Structural Biotechnology Journal",
  year="2019",
  volume="17",
  number="1",
  pages="118--126",
  doi="10.1016/j.csbj.2018.12.006",
  issn="2001-0370",
  url="http://www.sciencedirect.com/science/article/pii/S2001037018301223"
}