Reference-free Identification of Phage DNA Using Signal Processing on Nanopore Data

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F17%3APU125197" target="_blank" >RIV/00216305:26220/17:PU125197 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1109/BIBE.2017.00-71" target="_blank" >http://dx.doi.org/10.1109/BIBE.2017.00-71</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1109/BIBE.2017.00-71" target="_blank" >10.1109/BIBE.2017.00-71</a>

Result language
angličtina
Original language name
Reference-free Identification of Phage DNA Using Signal Processing on Nanopore Data
Original language description
Nanopore sequencing has become an invaluable aid in small sequencing projects. Thanks to its compact size, the Oxford Nanopore MinION platform is often used in crisis situations, such as outbreaks of microbial infections, to determine the causes of the problem. As a platform that produces data in real-time, it requires bioinformatics techniques designed for fast data processing. In this paper, we demonstrate the possibility of the direct processing of nanopore current signals, the so-called squiggles, for fast reference-free identification of phage DNA. The proposed technique is based on the computation of Hjorth parameters and is suitable for fast visualization of the data, as well as for proper classification by many machine learning algorithms. The classification of the data also raises the possibility of applying adapted base calling algorithms for both groups separately, as phage and host DNA have different features.
Czech name
—
Czech description
—

Project
<a href="/en/project/GA17-01821S" target="_blank" >GA17-01821S: High throughput bacterial genome assembly and annotation techniques using genomic signal processing</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2017
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Article name in the collection
2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017
ISBN
978-1-5386-1324-5
ISSN
—
e-ISSN
—
Number of pages
584
Pages from-to
101-105
Publisher name
Conference Publishing Services
Place of publication
Washington DC
Event location
Washington DC
Event date
Oct 23, 2017
Type of event by nationality
WRD - Celosvětová akce
UT code for WoS article
000427878000017

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