Comput Biol Chem - Deposition and extension approach to find longest common subsequence for thousands of long sequences.

Tópicos

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Resumo

The problem of finding the longest common subsequence (LCS) for an arbitrary number 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, Expansion Algorithm and THSB. However, the performance, either in result quality or in process time, 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 "sequence deposition" based on fine tuning of search range, and then extends this common subsequence. The algorithm is proven to generate Common Subsequences (CSs) with guaranteed lengths. The experiments on different dataset showed that the results of DEA algorithm were better than those of Long Run and Expansion Algorithm, especially on many long sequences. The algorithm also had superior efficiency both in time and memory space.

Resumo Limpo

problem find longest common subsequ lcs arbitrari number sequenc interest challeng problem comput scienc problem npcomplet import mani heurist algorithm propos long run expans algorithm thsb howev perform either result qualiti process time mani current heurist algorithm deterior fast number sequenc sequenc length increas paper propos postprocess heurist algorithm lcs problem deposit extens algorithm dea algorithm first generat common subsequ sequenc deposit base fine tune search rang extend common subsequ algorithm proven generat common subsequ css guarante length experi differ dataset show result dea algorithm better long run expans algorithm especi mani long sequenc algorithm also superior effici time memori space

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