Department of Computer Engineering, Kyung Hee University, Gyeonggi-do, Yongin-si, Republic of Korea.
Evol Bioinform Online. 2013 Jul 7;9:251-61. doi: 10.4137/EBO.S12160. Print 2013.
Effective representation of DNA sequences is one of the important tasks in the study of genome sequences. In this paper, we propose a graphical representation of DNA sequences based on nucleotide ring structure. In the proposed representation, we convert DNA sequences into 16 dinucleotides on the surface of the hexagon so that it can preserve nucleotide's chemical property and positional information. Our approach can provide capability of efficient similarity comparison between DNA sequences and also high comparison accuracy. Furthermore, our approach satisfies uniqueness and no degeneracy of DNA sequences. In the experimental study, we use phylogeny analysis for evolutionary relationship among different species. Extensive performance study shows that the proposed method can give better performance than existing methods in comparison with the degree of similarity.
有效表示 DNA 序列是基因组序列研究中的重要任务之一。在本文中，我们提出了一种基于核苷酸环结构的 DNA 序列图形表示方法。在提出的表示方法中，我们将 DNA 序列转换为六边形表面上的 16 个二核苷酸，从而可以保留核苷酸的化学性质和位置信息。我们的方法可以提供 DNA 序列之间高效相似性比较的能力，并且具有较高的比较准确性。此外，我们的方法满足 DNA 序列的唯一性和非简并性。在实验研究中，我们使用系统发育分析来研究不同物种之间的进化关系。广泛的性能研究表明，与相似性程度相比，所提出的方法在比较中可以提供更好的性能。
