can evolve, making its primary sequence structure slightly

There are three evolution events which may happen through an

process. They are the residue substitution, which is also called

ion, the insertion and the deletion of a residue or a segment within

ce [Tseng, et al., 2006; Rivas, et al., 2008]. The latter two are also

e indel process. A residue substitution means the replacement of

i.e., an existing nucleic acid or an amino acid has been replaced

nucleic acid or a new amino acid in an evolution. For instance,

nd residue of LGPSSKQT has been mutated from G to S in an

leading to a new sequence LSPSSKQT.

ndel stands for two scenarios. First, new residue(s) is introduced

quence through an evolution process. This is called the insertion.

residue(s) is missing through an evolution process. This is called

on. Suppose an original sequence is LGPSSKQT. Its evolutionary

may be in the format as LGPSSCKQT. Therefore a new residue

duced between S and K through an evolution process. One of the

ts between these two sequences is shown below, where a gap

by a hyphen key is inserted in the ancestor sequence for it to be

with its descendant sequence for introducing the residue C in the

nt sequence.

KQT

|||

KQT

ose a deletion happens to the ancestor sequence LGPSSKQT

olution and this has caused two missing consecutive residues (the

the sixth, i.e., S and K) from the ancestor sequence. One of the

ts for them is shown below, where two hyphen keys are inserted

scendant sequence to denote two deletions (lost residues) which

pened to its ancestor sequence in an evolution.