Set of rules for genomic signal downsampling

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00159816%3A_____%2F16%3A00063108" target="_blank" >RIV/00159816:_____/16:00063108 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216305:26220/15:PU114531

Výsledek na webu

<a href="http://dx.doi.org/10.1016/j.compbiomed.2015.05.022" target="_blank" >http://dx.doi.org/10.1016/j.compbiomed.2015.05.022</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.compbiomed.2015.05.022" target="_blank" >10.1016/j.compbiomed.2015.05.022</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Set of rules for genomic signal downsampling

Popis výsledku v původním jazyce

Comparison and classification of organisms based on molecular data is an important task of computational biology, since at least parts of DNA sequences for many organisms are available. Unfortunately, methods for comparison are computationally very demanding, suitable only for short sequences. In this paper, we focus on the redundancy of genetic information stored in DNA sequences. We proposed rules for downsampling of DNA signals of cumulated phase. According to the length of an original sequence, we are able to significantly reduce the amount of data with only slight loss of original information. Dyadic wavelet transform was chosen for fast downsampling with minimum influence on signal shape carrying the biological information. We proved the usability of such new short signals by measuring percentage deviation of pairs of original and downsampled signals while maintaining spectral power of signals. Minimal loss of biological information was proved by measuring the Robinson-Foulds distance between pairs of phylogenetic trees reconstructed from the original and downsampled signals. The preservation of inter-species and intra-species information makes these signals suitable for fast sequence identification as well as for more detailed phylogeny reconstruction.

Název v anglickém jazyce

Set of rules for genomic signal downsampling

Popis výsledku anglicky

Comparison and classification of organisms based on molecular data is an important task of computational biology, since at least parts of DNA sequences for many organisms are available. Unfortunately, methods for comparison are computationally very demanding, suitable only for short sequences. In this paper, we focus on the redundancy of genetic information stored in DNA sequences. We proposed rules for downsampling of DNA signals of cumulated phase. According to the length of an original sequence, we are able to significantly reduce the amount of data with only slight loss of original information. Dyadic wavelet transform was chosen for fast downsampling with minimum influence on signal shape carrying the biological information. We proved the usability of such new short signals by measuring percentage deviation of pairs of original and downsampled signals while maintaining spectral power of signals. Minimal loss of biological information was proved by measuring the Robinson-Foulds distance between pairs of phylogenetic trees reconstructed from the original and downsampled signals. The preservation of inter-species and intra-species information makes these signals suitable for fast sequence identification as well as for more detailed phylogeny reconstruction.

Druh

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

CEP obor

FP - Ostatní lékařské obory

OECD FORD obor

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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

2016

Kód důvěrnosti údajů

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

Název periodika

Computers in Biology and Medicine

ISSN

0010-4825

e-ISSN

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Svazek periodika

69

Číslo periodika v rámci svazku

FEB

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

7

Strana od-do

308-314

Kód UT WoS článku

000371188400033

EID výsledku v databázi Scopus

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