Publication detail

Use of whole genome DNA spectrograms in bacterial classification

KUBICOVÁ, V. PROVAZNÍK, I.

Original Title

Use of whole genome DNA spectrograms in bacterial classification

Type

journal article in Web of Science

Language

English

Original Abstract

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.

Keywords

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

Authors

KUBICOVÁ, V.; PROVAZNÍK, I.

RIV year

2015

Released

9. 5. 2015

Publisher

Elsevier

ISBN

0010-4825

Periodical

COMPUTERS IN BIOLOGY AND MEDICINE

Year of study

69

Number

February 2016

State

United States of America

Pages from

298

Pages to

307

Pages count

10

URL

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

Full text in the Digital Library

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"
}