Abstract: This paper proposes a pre-merged repeats masking-off method by studying repeats analysis in DNA fragment assembly. The method can recognize and merge the different shotgun fragments owning the same overlap substring by scanning the shotgun set, and mark the position of the repeats and masking-off them before DNA fragment assembly. Simulations show that the rate of false repeats recognition with the method is descended, and CPU time of DNA fragment assembly is reduced because of pre-merged method.

Key words: fragment assembly, pre-merged, repeats, masking-off

摘要： 针对DNA片段拼接中的重复序列识别及屏蔽问题，提出一种预归并重复序列屏蔽方法。在片段拼接前通过扫描子串标识出可能存在重叠关系的shotgun片段，利用子串归并该相关片段，标识出重复序列的位置信息，达到屏蔽的目的。计算机模拟分析表明，该方法识别重复序列的错误率低，通过预归并有效缩减了shotgun集合的规模，降低了拼接时的计算复杂度。

关键词: 片段拼接, 预归并, 重复序列, 屏蔽

CLC Number: 

• N945