Detail publikačního výsledku

Prokaryotic DNA Signal Downsampling for Fast Whole Genome Comparison

SEDLÁŘ, K.; ŠKUTKOVÁ, H.; VÍTEK, M.; PROVAZNÍK, I.

Originální název

Prokaryotic DNA Signal Downsampling for Fast Whole Genome Comparison

Anglický název

Prokaryotic DNA Signal Downsampling for Fast Whole Genome Comparison

Druh

Článek Scopus

Originální abstrakt

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 them extremely 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 warping (DTW).

Anglický abstrakt

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 them extremely 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 warping (DTW).

Klíčová slova

prokaryotes, genomic signal, cumulated phase, compression, classification, dwt, dtw

Klíčová slova v angličtině

prokaryotes, genomic signal, cumulated phase, compression, classification, dwt, dtw

Autoři

SEDLÁŘ, K.; ŠKUTKOVÁ, H.; VÍTEK, M.; PROVAZNÍK, I.

Rok RIV

2015

Vydáno

01.06.2014

Nakladatel

Springer International Publishing

Místo

Německo

ISSN

2194-5357

Periodikum

Advances in Intelligent Systems and Computing

Svazek

283

Číslo

6

Stát

Švýcarská konfederace

Strany od

373

Strany do

383

Strany počet

11

BibTex

@article{BUT107893,
  author="Karel {Sedlář} and Helena {Vítková} and Martin {Vítek} and Valentýna {Provazník}",
  title="Prokaryotic DNA Signal Downsampling for Fast Whole Genome Comparison",
  journal="Advances in Intelligent Systems and Computing",
  year="2014",
  volume="283",
  number="6",
  pages="373--383",
  doi="10.1007/978-3-319-06593-9\{_}33",
  issn="2194-5357"
}