Detail publikačního výsledku

Progressive alignment of genomic signals by multiple dynamic time warping

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

Originální název

Progressive alignment of genomic signals by multiple dynamic time warping

Anglický název

Progressive alignment of genomic signals by multiple dynamic time warping

Druh

Článek WoS

Originální abstrakt

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.

Anglický abstrakt

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.

Klíčová slova

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

Klíčová slova v angličtině

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

Autoři

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

Rok RIV

2016

Vydáno

21.11.2015

Nakladatel

Elsevier

ISSN

0022-5193

Periodikum

JOURNAL OF THEORETICAL BIOLOGY

Svazek

2015

Číslo

385

Stát

Spojené státy americké

Strany od

20

Strany do

30

Strany počet

11

URL

http://authors.elsevier.com/sd/article/S0022519315003951

Plný text v Digitální knihovně

http://hdl.handle.net/11012/69205

BibTex

@article{BUT116346,
  author="Helena {Vítková} and Martin {Vítek} and Karel {Sedlář} and Valentýna {Provazník}",
  title="Progressive alignment of genomic signals by multiple dynamic time warping",
  journal="JOURNAL OF THEORETICAL BIOLOGY",
  year="2015",
  volume="2015",
  number="385",
  pages="20--30",
  doi="10.1016/j.jtbi.2015.08.007",
  issn="0022-5193",
  url="http://authors.elsevier.com/sd/article/S0022519315003951"
}

Dokumenty

1-s2.0-S0022519315003951-main