Use of whole genome DNA spectrograms in bacterial classification
The result's identifiers
Result code in 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>
Alternative codes found
RIV/00216305:26220/15:PU114501
Result on the web
<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>
Alternative languages
Result language
angličtina
Original language name
Use of whole genome DNA spectrograms in bacterial classification
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
FS - Medical facilities, apparatus and equipment
OECD FORD branch
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Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2016
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Computers in Biology and Medicine
ISSN
0010-4825
e-ISSN
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Volume of the periodical
69
Issue of the periodical within the volume
FEB
Country of publishing house
GB - UNITED KINGDOM
Number of pages
10
Pages from-to
298-307
UT code for WoS article
000371188400032
EID of the result in the Scopus database
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