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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F19%3APU130319" target="_blank" >RIV/00216305:26220/19:PU130319 - isvavai.cz</a>

Result on the web

<a href="http://www.sciencedirect.com/science/article/pii/S2001037018301223" target="_blank" >http://www.sciencedirect.com/science/article/pii/S2001037018301223</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.csbj.2018.12.006" target="_blank" >10.1016/j.csbj.2018.12.006</a>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

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

Project

<a href="/en/project/GA17-01821S" target="_blank" >GA17-01821S: High throughput bacterial genome assembly and annotation techniques using genomic signal processing</a><br>

Continuities

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

Publication year

2019

Confidentiality

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

Name of the periodical

Computational and Structural Biotechnology Journal

ISSN

2001-0370

e-ISSN

—

Volume of the periodical

17

Issue of the periodical within the volume

1

Country of publishing house

SE - SWEDEN

Number of pages

9

Pages from-to

118-126

UT code for WoS article

000504205700013

EID of the result in the Scopus database

2-s2.0-85060238359