无比对的生物分子序列比较方法

生物序列分析是生物信息学的主要研究领域,常常通过比较分析获取有用的信息。最常用的比较方法是序列比对,但是利用比对的序列比较假设了同源片断之间是邻接保守的,这和遗传重组相冲突,而且多序列比对在计算复杂性等方面存在困难,这些使得人们努力研究无比对的序列比较方法。本文综述了目前无比对序列比较的两类主要方法:一类基于字(低聚物)的出现率及其分布,通过出现率向量定义的笛卡尔空间中的距离计算来实现序列比较;另一类使用柯尔莫哥洛夫复杂度理论或混沌理论来实现序列比较。

Alignment-free Biomolecular Sequence Comparison Method

Biosequence analysis is the primary research field of bioinformatics. In this field, useful information can be extracted by comparison analysis methods. Among them, sequence alignment is the most common comparison method. However the sequence comparison by alignment, which assumes conservation of contiguity between homologous segments, is at odds with genetic recombination. Especially for the multisequence alignment, there exists the difficulty in the complexity of calculation. Therefore, alignment-free sequence comparison methods are required. In this paper, two main categories of alignment-free sequence comparison methods are reviewed. The first one is based on the word (oligomer) frequency and its distribution. The sequences are compared using the distances defined in a Cartesian space by the frequency vectors. In the second category, sequences are compared using Kolmogorov complexity and chaos theory.