On the Twin DNA Sequences Assembly Problem

• Main Authors: Chen-Wei Chen, 陳震威
• Other Authors: Richard Chia-Tung Lee
• Format: Others
• Language: en_US
• Published: 2006
• Online Access: http://ndltd.ncl.edu.tw/handle/38674906313255318206

碩士 === 國立暨南國際大學 === 資訊工程學系 === 94 === The twin DNA sequences are two complementary sequences. The problem of this thesis is defined as follows: Given a set of strings S={S1, S2, …, Sn} which are cut from two complementary sequences X and Y by using the shotgun method. Both X and Y are cut twice. All positions of breaking X or Y are distinct. Our job is to reconstruct the original two sequences, X and Y, from S. An algorithm is proposed in this thesis. Our algorithm can be viewed as a tree searching strategy. We also propose three properties. The complementary DNA sequences constructed by our algorithm must satisfy the three properties. For each selected fragment x, we find all of the fragments which overlap with x. We select the fragment y whose length of overlapping with x is longest as the next fragment. If any one of the three properties is transgressed, we have to perform a backtracking. Finally, our experiments successfully reconstructed the original sequences.