On global sequence alignment

On global sequence alignment

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Article ID: iaor2000878
Country: United States
Volume: 10
Issue: 3
Start Page Number: 227
End Page Number: 235
Publication Date: Jul 1994
Journal: Computer Applications in the Biosciences
Authors:
Keywords: programming: dynamic
Abstract:

We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time. We also describe a multiple alignment algorithm based on the pairwise algorithm. Both algorithms have been implemented as portable C programs. Experimental results indicate that for a commonly used set of gap penalties, the new programs produce more satisfactory alignments on sequences of various lengths than some existing pairwise and multiple programs based on the dynamic programming algorithm of Needleman and Wunsch.

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