The Statistics of Repeats

在马尔可夫加性过程(MAP)中，不精确的简单重复可以被量化为局部和。局部和的最大值具有渐近的Gumbel分布，这是由一般映射公式给出的。一般的MAP公式通常在计算上很难处理，但在重复情况下的基本简化允许从维度等于相关字母表大小的矩阵计算Gumbel参数。我对无间隔重复序列的分析结果比G.Achaz等人通过模拟得出的结果更详细。(2006)RepSeek，一个从大DNA序列中检索近似重复的工具。生物信息学。用Ruzzo-Tompa算法寻找重复序列，然后评估结果的程序的工作原型在NCBI内部可用。Martin Frith目前正在将我们的不精确无间隙重复代码实现为一个检测基因组重复的工具。我们在量化有差距的重复序列的统计数据方面也取得了重大进展。

Inexact simple repeats can be quantified as local sums in a Markov additive process (MAP). The maximum of the local sums has an asymptotic Gumbel distribution, which are given by general MAP formulas. The general MAP formulas are usually computationally intractable, but an essential simplification in the case of repeats permits the Gumbel parameters to be computed from matrices whose dimension equals the size of the relevant alphabet. My analytic results for ungapped repeats are more detailed than those derived by simulation in G. Achaz et al. (2006) Repseek, a tool to retrieve approximate repeats from large DNA sequences. Bioinformatics. A working prototype of program for finding repeats with the Ruzzo-Tompa algorithm and then evaluating the results is available internally, within NCBI. Martin Frith is currently implementing our code for inexact gapless repeats into a tool for detecting genomic repeats. We are also making significant progress in quantifying the statistics of gapped repeats.