DNA片段拼接中基于定长特征子串的重复序列信息屏蔽方法

Definite-sized Characteristic Substrings Based Method for the Masking-off of Repeats in DNA Fragment Assembly

包含重复序列(repeats)的DNA序列的重构是大规模DNA片段拼接所面临的实际困难之一。在考虑片段数据所隐含的位置信息的基础上,提出了一种基于定长特征子串的屏蔽片段数据中重复序列信息的方法,即在进行序列相互比对前利用独特子串标识大多数片段,从而减少可能的错误重叠,讨论了方法中几个参数的确定问题并用计算结果说明了方法的有效性。

One of the practical difficulties that remains in large-scale DNA fragment assembly is the correct reconstruction of DNA sequences including repeats. An approach based on the definite-sized characteristic substring for the masking-off of repeats is proposed after considering the relative position information contained in fragment data. Before pair-wise alignment the approach chose unique substrings to mark fragments for the sake of decrease in possible incorrect overlaps. We also concretely describes the determination of some parameters and finally presents the computational result to prove the effectiveness of the method.