| 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 |
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| 引用本文： | 张博锋,王正华.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[J].国防科技大学学报,2002,24(6):67-70. |
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| 作者姓名： | 张博锋 王正华 |
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| 作者单位： | 国防科技大学并行与分布处理国家重点实验室,湖南,长沙,410073 |
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| 基金项目： | 国家自然科学基金资助重点项目(69933030) |
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| 摘 要： | 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。
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| 关 键 词： | 生物信息学 片段拼接 重复片段 屏蔽 定长特征子串 |
| 文章编号： | 1001-2486(2002)06-0067-04 |
| 收稿时间： | 2002/7/12 0:00:00 |
| 修稿时间： | 2002年7月12日 |
Definite-sized Characteristic Substrings Based Method for the Masking-off of Repeats in DNA Fragment Assembly |
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| ZHANG Bofeng and WANG Zhenghua.Definite-sized Characteristic Substrings Based Method for the Masking-off of Repeats in DNA Fragment Assembly[J].Journal of National University of Defense Technology,2002,24(6):67-70. |
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| Authors: | ZHANG Bofeng and WANG Zhenghua |
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| Affiliation: | National Laboratory for Parallel & Distributed Processing, National Univ. of Defense Technology, Changsha 410073, China;National Laboratory for Parallel & Distributed Processing, National Univ. of Defense Technology, Changsha 410073, China |
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| Abstract: | 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. |
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| Keywords: | bioinformatics fragment assembly repeats masking-off definite-sized characteristic substring |
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