Biogeometry Research Faster Multiple Sequence Alignment Algorithms Based on Pairwise Segmentation
نویسندگان
چکیده
Multiple Sequence Alignment (MSA) is a central problem in computational molecular biology --it identifies and quantifies similarities among several protein or DNA sequences.The well-known dynamic programming (DP) algorithms align k sequences (each of length n) by constructing a k-dimensional grid graph of size O(nk), with each of the sequences enumerating one of the dimensions of the grid. The optimal MSA is an optimal path from (n,...,n) to (0,...,0). Unfortunately, the exponential running time makes this approach prohibitive even for modest values of n and k. There is little hope for improving the worst-case efficiency of an algorithm for this problem since the MSA problem is NP-Hard [1]. However, the sequences constructed in the lowerbound constructions are not representative of protein and DNA sequences abundant in nature, and the alignments are not reminiscent of ones studied in practice. This led to the question whether faster algorithms could be developed for protein and DNA sequences.
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