Deposition and Extension Approach to Find Longest Common Subsequence for Multiple Sequences

TL;DR

This paper introduces the Deposition and Extension Algorithm (DEA), a heuristic method for finding the longest common subsequence in multiple sequences, which outperforms existing algorithms in accuracy and efficiency, especially with long sequences.

Contribution

The paper presents a novel heuristic algorithm for LCS that guarantees subsequence length and improves performance over existing methods on large, long sequences.

Findings

DEA outperforms Long Run and Expansion algorithms in accuracy.

DEA has better efficiency in time and space.

Results are especially improved for many long sequences.

Abstract

The problem of finding the longest common subsequence (LCS) for a set of sequences is a very interesting and challenging problem in computer science. This problem is NP-complete, but because of its importance, many heuristic algorithms have been proposed, such as Long Run algorithm and Expansion algorithm. However, the performance of many current heuristic algorithms deteriorates fast when the number of sequences and sequence length increase. In this paper, we have proposed a post process heuristic algorithm for the LCS problem, the Deposition and Extension algorithm (DEA). This algorithm first generates common subsequence by the process of sequences deposition, and then extends this common subsequence. The algorithm is proven to generate Common Subsequences (CSs) with guaranteed lengths. The experiments show that the results of DEA algorithm are better than those of Long Run and Expansion algorithm, especially on many long sequences. The algorithm also has superior efficiency both in time and space.