Sequence Comparison using Multi-Order Markov Chains

摘要：

DNA sequences are often found to be composed of locally homogeneous segments that are functionally important. Most sequence comparison methods do not consider such a compositional property. We introduce a new method that takes this issue into consideration. With our method, the information of a DNA sequence is first transformed into a multi-order transition matrix (MTM); the resulting matrices are then used to compute pair-wise distances; and the consequent distances are used to construct molecular phylogeny. Experiments with both simulated and real datasets show that the proposed method is able to reconstruct phylogenies consistent with those pre-defined or commonly accepted phylogenies.

作者: Xiang Fang Guoqing Lu Shunpu Zhang

作者单位: Department of Statistics University of Nebraska Lincoln Lincoln, NE 68583-0963, USA Department of Biology University of Nebraska at Omaha Omaha, NE 68182-0040

会议类型: 国际会议

会议名称: The 4th International Conference on Bioinformatics and Biomedical Engineering(第四届IEEE生物信息与生物医学工程国际会议 iCBBE 2010)

会议地点: 成都

会议语种:英文

页码: 1-5

在线出版日期: 2010-06-18（万方平台首次上网日期，不代表论文的发表时间）