Two Dimensional Yau-Hausdorff Distance with Applications on Comparison of DNA and Protein Sequences.
Two Dimensional Yau-Hausdorff Distance with Applications on Comparison of DNA and Protein Sequences.
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DOI：
10.1371/journal.pone.0136577
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Yau SS
中科院分区：
文献类型：
--
作者：
Tian K;Yang X;Kong Q;Yin C;He RL;Yau SS
比较DNA或蛋白质序列在基因组的功能分析中起着重要作用。尽管有许多方法可用于序列比较，但很少有方法保留序列的信息内容。我们提出了一种新的方法，Yau-Hausdorff方法，它考虑了所有的平移和旋转时，寻求最佳匹配的DNA或蛋白质序列的图形曲线。该方法的复杂度低于任何二维最小Hausdorff算法。Yau-Hausdorff方法可用于基于两个重要工具的DNA序列相似性度量：Yau-Hausdorff距离和DNA序列的图形表示。DNA序列的图形表示保存了所有的序列信息，数学上证明了Yau-Hausdorff距离是一个真正的度量。因此，提出的距离可以精确地度量DNA序列的相似性。DNA序列的Yau-Hausdorff距离的系统发育分析表明，我们的方法在DNA或蛋白质序列的相似性比较的准确性和稳定性。这项研究表明，Yau-Hausdorff距离是一个自然的度量的DNA和蛋白质序列具有高水平的稳定性。该方法也可以应用于蛋白质序列的相似性分析的图形表示，以及一般的二维形状匹配。
Comparing DNA or protein sequences plays an important role in the functional analysis of genomes. Despite many methods available for sequences comparison, few methods retain the information content of sequences. We propose a new approach, the Yau-Hausdorff method, which considers all translations and rotations when seeking the best match of graphical curves of DNA or protein sequences. The complexity of this method is lower than that of any other two dimensional minimum Hausdorff algorithm. The Yau-Hausdorff method can be used for measuring the similarity of DNA sequences based on two important tools: the Yau-Hausdorff distance and graphical representation of DNA sequences. The graphical representations of DNA sequences conserve all sequence information and the Yau-Hausdorff distance is mathematically proved as a true metric. Therefore, the proposed distance can preciously measure the similarity of DNA sequences. The phylogenetic analyses of DNA sequences by the Yau-Hausdorff distance show the accuracy and stability of our approach in similarity comparison of DNA or protein sequences. This study demonstrates that Yau-Hausdorff distance is a natural metric for DNA and protein sequences with high level of stability. The approach can be also applied to similarity analysis of protein sequences by graphic representations, as well as general two dimensional shape matching.