title: Progressive alignment of genomic signals by multiple dynamic time warping.
abstract: This paper presents the utilization of progressive alignment principle for positional adjustment of a set of genomic signals with different lengths. The new method of multiple alignment of signals based on dynamic time warping is tested for the purpose of evaluating the similarity of different length genes in phylogenetic studies. Two sets of phylogenetic markers were used to demonstrate the effectiveness of the evaluation of intraspecies and interspecies genetic variability. The part of the proposed method is modification of pairwise alignment of two signals by dynamic time warping with using correlation in a sliding window. The correlation based dynamic time warping allows more accurate alignment dependent on local homologies in sequences without the need of scoring matrix or evolutionary models, because mutual similarities of residues are included in the numerical code of signals.
authors: Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic. Electronic address: skutkova@feec.vutbr.cz.
authors: Helena
authors: H
authors: Skutkova
authors: 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: vitek@feec.vutbr.cz.
authors: Martin
authors: M
authors: Vitek
authors: Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic. Electronic address: sedlar@feec.vutbr.cz.
authors: Karel
authors: K
authors: Sedlar
authors: 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: Ivo
authors: I
authors: Provaznik
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D012815:Signal Processing, Computer-Assisted; D013045:Species Specificity
chemical_list: D012329:RNA, Bacterial; D012337:RNA, Ribosomal, 18S
keywords: Correlation; Genomic signal processing; Multiple alignment; Phylogenetic tree; Similarity distance