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. 1994 Jun;10(3):227-35.
doi: 10.1093/bioinformatics/10.3.227.

On global sequence alignment

X Huang  1
Affiliations

On global sequence alignment

X Huang. Comput Appl Biosci. 1994 Jun.

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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