he alignment gap

nd issue of sequence homology alignment is the alignment gap.

nment algorithm has to satisfy the following requirements.

two sequences without inserted a gap may not work properly,

y when an indel event has happened. This is because two

s definitely have different lengths when an indel event has

d. For instance, the evolution of the ancestor sequence

QT to the descendant sequence LGPSQT has resulted in

s with different lengths. Without introducing gaps, aligning these

uences will not generate a meaningful alignment. Of course,

two sequences with too many gaps is also unacceptable.

e, an alignment should maximise the number of the aligned pairs

mise the number of the inserted gaps. A gap penalty, which can

the impact of gap insertion on an alignment performance, has

been introduced for this purpose in almost every alignment

m.

he alignment strategy

issue of sequence homology alignment is the alignment strategy.

e mainly two strategies, i.e., the global homology alignment and

homology alignment [Polyanovsky, et al., 2011; Pollard, et al.,

global homology alignment process employs all the residues

sequences to generate an alignment model. The alignment shown

such a global alignment,

QTGKGS-SRIWDN

| ||| | |

QAGKGAIMRLGDA

al homology alignment may align the above two sequences by

g only subsets of residues from two sequences. One possibility

ng two above sequences is shown below, where only five pairs