利用核苷酸分布均匀性鉴定DNA序列中的重复序列
Identification of repeats in DNA sequences using nucleotide distribution uniformity
摘要：
重复序列在基因组结构、功能和调控中具有重要意义，但目前还没有完全有效的方法来精确鉴定DNA序列中的重复序列，重复序列与基因组周期性之间的关系也不清楚。我们提出了一个$\textit{ab initio}$方法来定量检测重复元件和推断重复元件中的一致重复模式。该方法使用DNA序列或基因组中周期性位置处的核苷酸分布均匀性的测量。它可以识别周期性，一致重复模式，拷贝数和重复元件的完美水平。在不同的DNA序列和基因组上使用该方法的结果证明了在识别重复模式和周期性方面的有效性和准确性。该方法的复杂度与所分析序列的长度成线性关系。
英文摘要：
Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive elements and periodicities of genomes is not clearly understood. We present an $\textit{ab initio}$ method to quantitatively detect repetitive elements and infer the consensus repeat pattern in repetitive elements. The method uses the measure of the distribution uniformity of nucleotides at periodic positions in DNA sequences or genomes. It can identify periodicities, consensus repeat patterns, copy numbers and perfect levels of repetitive elements. The results of using the method on different DNA sequences and genomes demonstrate efficacy and accuracy in identifying repeat patterns and periodicities. The complexity of the method is linear with respect to the lengths of the analyzed sequences.
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