Use of whole genome DNA spectrograms in bacterial classification

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00159816%3A_____%2F16%3A00063021" target="_blank" >RIV/00159816:_____/16:00063021 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216305:26220/15:PU114501

Výsledek na webu

<a href="http://dx.doi.org/10.1016/j.compbiomed.2015.04.038" target="_blank" >http://dx.doi.org/10.1016/j.compbiomed.2015.04.038</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.compbiomed.2015.04.038" target="_blank" >10.1016/j.compbiomed.2015.04.038</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Use of whole genome DNA spectrograms in bacterial classification

Popis výsledku v původním jazyce

A spectrogram reflects the arrangement of nucleotides through the whole chromosome or genome. Our previous study suggested that the spectrogram of whole genome DNA sequences is a suitable tool for the determination of relationships among bacteria. Related bacteria have similar spectrograms, and similarity in spectrograms was measured using a color layout descriptor. Several parameters, such as the mapping of four bases into a spectrogram, the number of considered elements in the color layout descriptor, the color model of the image and the building tree method, can be changed. This study addresses the use of parameter selection to ensure the best classification results. The quality of the classification was measured by Matthew's correlation coefficient (MCC). The proposed method with optimal parameters (called SpectCMP-Spectrogram CoMParison method) achieved an average MCC of 0.73 at the phylum level. The SpectCMP method was also tested at the order level; the average MCC in the classification of class Gammaproteobacteria was 0.76. The success of a classification with respect to the correct phyla was compared to three methods that are used in bacterial phylogeny: the CVTree method, OGTree method and moment vector method. The results show that the SpectCMP method can be used in bacterial classification at various taxonomic levels.

Název v anglickém jazyce

Use of whole genome DNA spectrograms in bacterial classification

Popis výsledku anglicky

A spectrogram reflects the arrangement of nucleotides through the whole chromosome or genome. Our previous study suggested that the spectrogram of whole genome DNA sequences is a suitable tool for the determination of relationships among bacteria. Related bacteria have similar spectrograms, and similarity in spectrograms was measured using a color layout descriptor. Several parameters, such as the mapping of four bases into a spectrogram, the number of considered elements in the color layout descriptor, the color model of the image and the building tree method, can be changed. This study addresses the use of parameter selection to ensure the best classification results. The quality of the classification was measured by Matthew's correlation coefficient (MCC). The proposed method with optimal parameters (called SpectCMP-Spectrogram CoMParison method) achieved an average MCC of 0.73 at the phylum level. The SpectCMP method was also tested at the order level; the average MCC in the classification of class Gammaproteobacteria was 0.76. The success of a classification with respect to the correct phyla was compared to three methods that are used in bacterial phylogeny: the CVTree method, OGTree method and moment vector method. The results show that the SpectCMP method can be used in bacterial classification at various taxonomic levels.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

FS - Lékařská zařízení, přístroje a vybavení

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

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

Rok uplatnění

2016

Kód důvěrnosti údajů

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

Název periodika

Computers in Biology and Medicine

ISSN

0010-4825

e-ISSN

—

Svazek periodika

69

Číslo periodika v rámci svazku

FEB

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

10

Strana od-do

298-307

Kód UT WoS článku

000371188400032

EID výsledku v databázi Scopus

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