All

What are you looking for?

All
Projects
Results
Organizations

Quick search

  • Projects supported by TA ČR
  • Excellent projects
  • Projects with the highest public support
  • Current projects

Smart search

  • That is how I find a specific +word
  • That is how I leave the -word out of the results
  • “That is how I can find the whole phrase”

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

  • Czech description

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

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

  • 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