Progressive alignment of genomic signals by multiple dynamic time warping
Progressive alignment of genomic signals by multiple dynamic time warping
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DOI：
10.1016/j.jtbi.2015.08.007
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发表时间：
2015-11-21
影响因子：
2
通讯作者：
Provaznik, Ivo
中科院分区：
文献类型：
--
作者：
Skutkova, Helena;Vitek, Martin;Provaznik, Ivo
本文提出了利用渐进比对原理对一组不同长度的基因组信号进行位置调整。为了在系统发育研究中评估不同长度基因的相似性，对基于动态时间规整的信号多重比对新方法进行了测试。使用两组系统发育标记来证明评估种内和种间遗传变异性的有效性。所提出的方法的一部分是修改的两个信号的两两对齐的动态时间弯曲使用相关的滑动窗口。基于相关性的动态时间规整允许依赖于序列中的局部同源性的更精确的比对，而不需要评分矩阵或进化模型，因为残基的相互相似性包括在信号的数字代码中。(C)2015作者出版社：Elsevier Ltd
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. (C) 2015 The Authors. Published by Elsevier Ltd.