Publication detail

Set of rules for genomic signal downsampling

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

Original Title

Set of rules for genomic signal downsampling

Czech Title

Soubor pravidel pro podvzorkování genomických signálů

English Title

Set of rules for genomic signal downsampling

Type

journal article

Language

en

Original Abstract

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.

Czech abstract

Porovnání a klasifikace organismů založená na molekulárních datech je důležitá část výpočetní biologie. V tomto článku jsme se zaměřili na redundanci genetické informace v DNA sekvencích.

English abstract

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.

Keywords

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

RIV year

2015

Released

04.06.2015

Publisher

Elsevier

Location

USA

Pages from

1

Pages to

7

Pages count

7

URL

Full text in the Digital Library

BibTex


@article{BUT115093,
  author="Karel {Sedlář} and Helena {Škutková} and Martin {Vítek} and Ivo {Provazník}",
  title="Set of rules for genomic signal downsampling",
  annote="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.",
  address="Elsevier",
  chapter="115093",
  doi="10.1016/j.compbiomed.2015.05.022",
  howpublished="online",
  institution="Elsevier",
  number="p1",
  volume="64",
  year="2015",
  month="june",
  pages="1--7",
  publisher="Elsevier",
  type="journal article"
}