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The '''sequential structure alignment program (SSAP)''' in [[chemistry]], [[physics]], and [[biology]] is a method that uses double [[dynamic programming]] to produce a structural alignment based on atom-to-atom [[Vector (geometric)|vectors]] in structure space.<ref>{{Cite journal
| last1 = Taylor | first1 = W. R.
| last2 = Orengo | first2 = C. A.
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| last1 = Orengo | first1 = C. A.
| last2 = Taylor | first2 = W. R.
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| series = Methods in Enzymology
| volume = 266
| pages = 617–635
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| doi=10.1016/s0076-6879(96)66038-8
| isbn = 9780121821678
}}</ref> Instead of the alpha carbons typically used in structural alignment, SSAP constructs its vectors from the [[beta carbon]]s for all residues except glycine, a method which thus takes into account the [[wikt:rotamer|rotameric state]] of each residue as well as its ___location along the backbone. SSAP works by first constructing a series of inter-residue distance vectors between each residue and its nearest non-contiguous neighbors on each protein. A series of matrices are then constructed containing the vector differences between neighbors for each pair of residues for which vectors were constructed. Dynamic programming applied to each resulting matrix determines a series of optimal local alignments which are then summed into a "summary" matrix to which dynamic programming is applied again to determine the overall structural alignment.
SSAP originally produced only pairwise alignments but has since been extended to multiple alignments as well.<ref name="taylor">{{Cite journal
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