Sequential and Non-Sequential alignments

LovoAlign is able to perform alignments for which one expects that the correspondence between atoms is sequential or not.

Sequential correspondences correspond to most Protein alignments, since one expects that if two residues are consecutive in one structure, they should be consecutive in the other structure. The bijection of a sequential alignment can be represented by the sequence-alignment, as in this case:

144	GSHMEEMIRSLQQRPEPT---WDLIHIAT	193
202	EE--LQ--KSIGHKPEPTDEEWELIKTVT	247

Non-sequential alignments are interesting when one do not expect such kind of regularity. For example, if the alignment of two ligands is considered, there is no rule on how the atoms of the ligands should be written or ordered in the structure files. Therefore, one should not expect that ATOM 1 from the first ligand correspond to ATOM 1 from the second ligand, nor any kind of sequentiality between the correspondence between the atoms. For cases like these, one should perform a non-sequential alignment. Non-sequential alignments are generally harder than sequential ones, so if one suspects that some sequentiality should be present, it is worth trying the sequential alternative always.