Skutkova Helena, Vitek Martin, Sedlar Karel, Provaznik Ivo
Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic.
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.
J Theor Biol. 2015 Nov 21;385:20-30. doi: 10.1016/j.jtbi.2015.08.007. Epub 2015 Aug 20.
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.
本文介绍了利用渐进比对原理对一组长度不同的基因组信号进行位置调整。基于动态时间规整的信号多重比对新方法，旨在评估系统发育研究中不同长度基因的相似性。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。所提方法的一部分是通过在滑动窗口中使用相关性，利用动态时间规整对两个信号进行成对比对的修改。基于相关性的动态时间规整允许根据序列中的局部同源性进行更准确的比对，而无需评分矩阵或进化模型，因为残基的相互相似性包含在信号的数字编码中。
