Publication detail

Progressive alignment of genomic signals by multiple dynamic time warping

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

Original Title

Progressive alignment of genomic signals by multiple dynamic time warping

English Title

Progressive alignment of genomic signals by multiple dynamic time warping

Type

journal article in Web of Science

Language

en

Original 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.

English 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.

Keywords

Genomic signal processing; Multiple alignment; Correlation; Phylogenetic tree; Similarity distance

RIV year

2015

Released

21.11.2015

Publisher

Elsevier

Pages from

20

Pages to

30

Pages count

11

URL

Full text in the Digital Library

BibTex


@article{BUT116346,
  author="Helena {Škutková} and Martin {Vítek} and Karel {Sedlář} and Ivo {Provazník}",
  title="Progressive alignment of genomic signals by multiple dynamic time warping",
  annote="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.",
  address="Elsevier",
  chapter="116346",
  doi="10.1016/j.jtbi.2015.08.007",
  howpublished="print",
  institution="Elsevier",
  number="385",
  volume="2015",
  year="2015",
  month="november",
  pages="20--30",
  publisher="Elsevier",
  type="journal article in Web of Science"
}