Detail publikace

Use of whole genome DNA spectrograms in bacterial classification

KUBICOVÁ, V. PROVAZNÍK, I.

Originální název

Use of whole genome DNA spectrograms in bacterial classification

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální abstrakt

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.

Klíčová slova

Relationships among bacteria; Whole genome comparison; SpectCMP method; DNA spectrogram; Spectrogram comparison

Autoři

KUBICOVÁ, V.; PROVAZNÍK, I.

Rok RIV

2015

Vydáno

9. 5. 2015

Nakladatel

Elsevier

ISSN

0010-4825

Periodikum

COMPUTERS IN BIOLOGY AND MEDICINE

Ročník

69

Číslo

February 2016

Stát

Spojené státy americké

Strany od

298

Strany do

307

Strany počet

10

URL

https://www.sciencedirect.com/science/article/pii/S0010482515001675

Plný text v Digitální knihovně

http://hdl.handle.net/11012/201333

BibTex

@article{BUT115067,
  author="Vladimíra {Kubicová} and Valentine {Provazník}",
  title="Use of whole genome DNA spectrograms in bacterial classification",
  journal="COMPUTERS IN BIOLOGY AND MEDICINE",
  year="2015",
  volume="69",
  number="February 2016",
  pages="298--307",
  doi="10.1016/j.compbiomed.2015.04.038",
  issn="0010-4825",
  url="https://www.sciencedirect.com/science/article/pii/S0010482515001675"
}