Benson G, Waterman M S
Department of Mathematics, University of Southern California, Los Angeles 90089-1113.
Nucleic Acids Res. 1994 Nov 11;22(22):4828-36. doi: 10.1093/nar/22.22.4828.
A significant portion of DNA consists of repeating patterns of various sizes, from very small (one, two and three nucleotides) to very large (over 300 nucleotides). Although the functions of these repeating regions are not well understood, they appear important for understanding the expression, regulation and evolution of DNA. For example, increases in the number of trinucleotide repeats have been associated with human genetic disease, including Fragile-X mental retardation and Huntington's disease. Repeats are also useful as a tool in mapping and identifying DNA; the number of copies of a particular pattern at a site is often variable among individuals (polymorphic) and is therefore helpful in locating genes via linkage studies and also in providing DNA fingerprints of individuals. The number of repeating regions is unknown as is the distribution of pattern sizes. It would be useful to search for such regions in the DNA database in order that they may be studied more fully. The DNA database currently consists of approximately 150 million basepairs and is growing exponentially. Therefore, any program to look for repeats must be efficient and fast. In this paper, we present some new techniques that are useful in recognizing repeating patterns and describe a new program for rapidly detecting repeat regions in the DNA database where the basic unit of the repeat has size up to 32 nucleotides. It is our hope that the examples in this paper will illustrate the unrealized diversity of repeats in DNA and that the program we have developed will be a useful tool for locating new and interesting repeats.
相当一部分DNA由各种大小的重复序列组成，从非常小的（一、二和三个核苷酸）到非常大的（超过300个核苷酸）。尽管这些重复区域的功能尚未完全了解，但它们对于理解DNA的表达、调控和进化似乎很重要。例如，三核苷酸重复序列数量的增加与人类遗传疾病有关，包括脆性X智力障碍和亨廷顿舞蹈症。重复序列在绘制和识别DNA方面也是一种有用的工具；特定模式在某一位置的拷贝数在个体间通常是可变的（多态性），因此有助于通过连锁研究定位基因，也有助于提供个体的DNA指纹。重复区域的数量以及模式大小的分布尚不清楚。在DNA数据库中搜索此类区域将有助于更全面地研究它们。目前的DNA数据库约由1.5亿个碱基对组成，并且呈指数级增长。因此，任何寻找重复序列的程序都必须高效且快速。在本文中，我们介绍了一些有助于识别重复模式的新技术，并描述了一个新程序，用于快速检测DNA数据库中重复区域，其中重复的基本单元大小可达32个核苷酸。我们希望本文中的例子能够说明DNA中尚未被认识到的重复序列的多样性，并且我们开发的程序将成为定位新的和有趣的重复序列的有用工具。
