Locating All Common Subsequences in Two DNA Sequences

Abstract

Biological sequence comparison is one of the most important and basic problems in computational biology. Due to its high demands for computational power and memory, it is a very challenging task. The well-known algorithm proposed by Smith-Waterman obtains the best local alignments at the expense of very high computing power and huge memory requirements. This paper introduces a new efficient algorithm to locate the longest common subsequences (LCS) in two different DNA sequences. It is based on the convolution between the two DNA sequences: The major sequence is represented in the linked-list X while the minor one is represented in circular linked-list Y. An array of linked lists is established where each linked list is corresponding to an element of the linked-list X and a new node is added to it for each match between the two sequences. If two or more matches in different locations in string Y share the same location in string X, the corresponding nodes will construct a unique linked-list. Accordingly, by the end of processing, we obtain a group of linked-lists containing nodes that reflect all possible matches between the two sequences X and Y. The proposed algorithm has been implemented and tested using C# language. The benchmark test shows very good speedups and indicated that impressive improvements has been achieved.