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

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

D - Stať ve sborníku

CEP obor

—

OECD FORD obor

10606 - Microbiology

Projekt

<a href="/cs/project/GA17-01821S" target="_blank" >GA17-01821S: Výkonnostní techniky pro sestavování a anotaci bakteriálního genomu využívající číslicové zpracování genomických signálů</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2017

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název statě ve sborníku

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering, BIBE 2017

ISBN

978-1-5386-1324-5

ISSN

—

e-ISSN

—

Počet stran výsledku

584

Strana od-do

101-105

Název nakladatele

Conference Publishing Services

Místo vydání

Washington DC

Místo konání akce

Washington DC

Datum konání akce

23. 10. 2017

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

000427878000017