title: Set of rules for genomic signal downsampling.
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.
authors.affiliation: Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic. Electronic address: sedlar@feec.vutbr.cz.
authors.forename: Karel
authors.initials: K
authors.lastname: Sedlar
authors.affiliation: Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic. Electronic address: skutkova@feec.vutbr.cz.
authors.forename: Helena
authors.initials: H
authors.lastname: Skutkova
authors.affiliation: International Clinical Research Center - Center of Biomedical Engineering, St. Anne׳s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic. Electronic address: vitek@feec.vutbr.cz.
authors.forename: Martin
authors.initials: M
authors.lastname: Vitek
authors.affiliation: Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic; International Clinical Research Center - Center of Biomedical Engineering, St. Anne׳s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic. Electronic address: provaznik@feec.vutbr.cz.
authors.forename: Ivo
authors.initials: I
authors.lastname: Provaznik
mesh_terms: D016678:Genome; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: Compression; Cumulated phase; DWT; Downsampling; Genomic signal; Phylogeny; Sequence identification