Prokaryotic DNA Signal Downsampling for Fast Whole Genome Comparison

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00159816%3A_____%2F14%3A00063532" target="_blank" >RIV/00159816:_____/14:00063532 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216305:26220/14:PU109293

Výsledek na webu

<a href="http://dx.doi.org/10.1007/978-3-319-06593-9_33" target="_blank" >http://dx.doi.org/10.1007/978-3-319-06593-9_33</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-3-319-06593-9_33" target="_blank" >10.1007/978-3-319-06593-9_33</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Prokaryotic DNA Signal Downsampling for Fast Whole Genome Comparison

Popis výsledku v původním jazyce

Classification of prokaryotes is mainly based on molecular data, since next-generation sequencing platforms provide fast and effective way to capture prokaryotes' characteristics. However, two different bacterial strains of the same genus can differ in the specific parts of their genomes due to copious amounts of repetitive and transposable parts. Thus, finding an ideal segment of genome for comparison is difficult. Conventional character-based methods rely on multiple sequence alignment, rendering themextremely computationally demanding. Only small parts of genomes can be compared in reasonable time. In this paper, we present a novel algorithm based on the conversion of the whole genome sequences to cumulative phase signals. Dyadic wavelet transform(DWT) is used for lossy compression of phase signals by eliminating redundant frequency bands. Signal classification is then performed as cluster analysis using Euclidean metrics where sequence alignment is replaced by dynamic time warpin

Název v anglickém jazyce

Prokaryotic DNA Signal Downsampling for Fast Whole Genome Comparison

Popis výsledku anglicky

Classification of prokaryotes is mainly based on molecular data, since next-generation sequencing platforms provide fast and effective way to capture prokaryotes' characteristics. However, two different bacterial strains of the same genus can differ in the specific parts of their genomes due to copious amounts of repetitive and transposable parts. Thus, finding an ideal segment of genome for comparison is difficult. Conventional character-based methods rely on multiple sequence alignment, rendering themextremely computationally demanding. Only small parts of genomes can be compared in reasonable time. In this paper, we present a novel algorithm based on the conversion of the whole genome sequences to cumulative phase signals. Dyadic wavelet transform(DWT) is used for lossy compression of phase signals by eliminating redundant frequency bands. Signal classification is then performed as cluster analysis using Euclidean metrics where sequence alignment is replaced by dynamic time warpin

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

EB - Genetika a molekulární biologie

OECD FORD obor

—

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

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

Rok uplatnění

2014

Kód důvěrnosti údajů

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

Název periodika

Advances in Intelligent Systems and Computing

ISSN

2194-5357

e-ISSN

—

Svazek periodika

283

Číslo periodika v rámci svazku

6

Stát vydavatele periodika

DE - Spolková republika Německo

Počet stran výsledku

11

Strana od-do

373-383

Kód UT WoS článku

000352133800034

EID výsledku v databázi Scopus

—