g

g

(

)

the alignments using both the Needleman-Wunsch algorithm and

h-Waterman algorithm was analysed for the sequences with

engths from 1,000 to 10,000. It can be seen in Figure 7.6 that the

e grows in an almost exponential rate along with the increased

length.

he CPU time spent on the alignment using the Needleman-Wunsch algorithm

mith-Waterman algorithm for sequences with variable lengths. The horizontal

for the sequence length.

s why it is required to investigate the alternatives for the sequence

on tasks. One of the candidates is the alignment-free sequence

on approach. The alignment-free sequence comparison approach

n 1980s [Blaisdell, 1986; Blaisdell, 1991]. The wide use of the

t-free sequence comparison approach is because of the time

ty of homology alignment algorithms. Most homology alignment

ms require residue-by-residue comparison between two sequences.

e complexity may not be so problematic for comparing a pair of

s. But it is definitely problematic when aligning one novel

against hundreds or thousands of known sequences.

42778 is a DNA sequence of SARS-CoV-2, which was revealed

Having understood that SARS-CoV-2 is similar to SARS-CoV in

% similarity [Caldaria, et al., 2020], how to find some similar

oV sequences to MT042778 in a database can be done using the

sequence comparison approach such as BLAST. BLAST