SE is a novel algorithm for deriving sequence alignment from a pair of superimposed structures. It does not use a gap penalty as the dynamic programming algorithm does and usually generates a more accurate alignment using less CPU time.
The SE algorithm first finds “seeds”, which are the pairs of residues, one from each structure, that meet certain stringent criteria for being structurally equivalent. Three consecutive seeds form a seed segment, which is extended along the diagonal of the alignment matrix in both directions. Distance and the amino acid type similarity between the residues are used to resolve conflicts that arise during extension of more than one diagonal. A detailed description of the algorithm can be found in BMC Bioinformatics 10 Suppl. 1:S4. The SE program can be downloaded from here.