Detail publikace

Set of rules for genomic signal downsampling

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

Originální název

Set of rules for genomic signal downsampling

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální abstrakt

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.

Klíčová slova

Genomic signal; Cumulated phase; Downsampling; Compression; DWT; Sequence identification; Phylogeny

Autoři

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

Rok RIV

2015

Vydáno

4. 6. 2015

Nakladatel

Elsevier

Místo

USA

ISSN

0010-4825

Periodikum

COMPUTERS IN BIOLOGY AND MEDICINE

Ročník

64

Číslo

p1

Stát

Spojené státy americké

Strany od

1

Strany do

7

Strany počet

7

URL

http://www.sciencedirect.com/science/article/pii/S0010482515002048

Plný text v Digitální knihovně

http://hdl.handle.net/11012/69200

BibTex

@article{BUT115093,
  author="Karel {Sedlář} and Helena {Vítková} and Martin {Vítek} and Valentine {Provazník}",
  title="Set of rules for genomic signal downsampling",
  journal="COMPUTERS IN BIOLOGY AND MEDICINE",
  year="2015",
  volume="64",
  number="p1",
  pages="1--7",
  doi="10.1016/j.compbiomed.2015.05.022",
  issn="0010-4825",
  url="http://www.sciencedirect.com/science/article/pii/S0010482515002048"
}