Progressive alignment of genomic signals by multiple dynamic time warping

Škutková, Helena; Vítek, Martin; Sedlář, Karel; Provazník, Ivo

Progressive alignment of genomic signals by multiple dynamic time warping

Files

1s2.0S0022519315003951main.pdf(1.09 MB)

Date

2015-11-21

Authors

Publisher

Elsevier

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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.
Článek se zabývý progresivním principem zarovnání setu různě dlouhých genomických signálů. Metoda je založená na dynamickém borcení časové osy. Výsledné genomické signály s přízpůsobenou délkou jsou použity pro fylogenetickou analýzu.

Keywords

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

Citation

Journal of Theoretical Biology. 2015, vol. 2015, issue 385, p. 20-30.
http://authors.elsevier.com/sd/article/S0022519315003951

Document type

Peer-reviewed

Document version

Published version

Language of document

en

Document licence

Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/4.0/