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A relative position based algorithm to find out the longest common subsequence from multiple biological sequences

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2 Author(s)
Shukla, A. ; Comput. Sci. & Eng. Dept., MNNIT Allahabad, Allahabad, India ; Agarwal, S.

The LCS problem is to find a subsequence that is common to two or more given sequences and is the longest one of such subsequences. This problem of searching the longest common subsequence (LCS) from multiple biological sequences is one of the most fundamental tasks in bioinformatics. In this paper, we present an easy and time efficient parallel algorithm based on calculating the relative positions of characters for finding out the LCS from any number of given DNA, RNA, Protein or general sequences. Here we give the example of DNA sequences, although this can be used for RNA, Protein or general sequences (provided we know the number of characters being used). The speed up in our LCS Algorithm is achieved through the pruning operations, in which we recognize and reject all those nucleotides which cannot generate the next character of the LCS thus reducing the search space and accelerating the search speed.

Published in:

Computer and Communication Technology (ICCCT), 2010 International Conference on

Date of Conference:

17-19 Sept. 2010