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SEDLÁŘ, K. ŠKUTKOVÁ, H. VÍTEK, M. PROVAZNÍK, I.
Originální název
Prokaryotic DNA Signal Downsampling for Fast Whole Genome Comparison
Typ
článek v časopise ve Scopus, Jsc
Jazyk
angličtina
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).
Klíčová slova
prokaryotes, genomic signal, cumulated phase, compression, classification, dwt, dtw
Autoři
SEDLÁŘ, K.; ŠKUTKOVÁ, H.; VÍTEK, M.; PROVAZNÍK, I.
Rok RIV
2014
Vydáno
1. 6. 2014
Nakladatel
Springer International Publishing
Místo
Německo
ISSN
2194-5357
Periodikum
Advances in Intelligent Systems and Computing
Ročník
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 Valentine {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" }