<s>
A	O
Pairwise	B-Algorithm
Algorithm	I-Algorithm
is	O
an	O
algorithmic	O
technique	O
with	O
its	O
origins	O
in	O
Dynamic	B-Algorithm
programming	I-Algorithm
.	O
</s>
<s>
Pairwise	B-Algorithm
algorithms	I-Algorithm
have	O
several	O
uses	O
including	O
comparing	O
a	O
protein	O
profile	O
(	O
a	O
residue	O
scoring	O
matrix	O
for	O
one	O
or	O
more	O
aligned	O
sequences	O
)	O
against	O
the	O
three	O
translation	O
frames	O
of	O
a	O
DNA	O
strand	O
,	O
allowing	O
frameshifting	O
.	O
</s>
<s>
For	O
normal	O
Protein-DNA	O
alignment	O
tools	O
,	O
they	O
first	O
choose	O
one	O
of	O
three	O
frames	O
to	O
translate	B-General_Concept
the	O
DNA	O
into	O
a	O
protein	O
sequence	O
,	O
and	O
then	O
compare	O
it	O
with	O
the	O
given	O
protein	O
.	O
</s>
<s>
The	O
PairWise	B-Algorithm
algorithm	I-Algorithm
is	O
a	O
variant	O
of	O
the	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
algorithm	I-Algorithm
best	O
local	B-Algorithm
alignment	I-Algorithm
algorithm	O
.	O
</s>
