<s>
In	O
bioinformatics	O
a	O
dot	B-Application
plot	I-Application
is	O
a	O
graphical	O
method	O
for	O
comparing	O
two	O
biological	O
sequences	O
and	O
identifying	O
regions	O
of	O
close	O
similarity	O
after	O
sequence	B-Algorithm
alignment	I-Algorithm
.	O
</s>
<s>
It	O
is	O
a	O
type	O
of	O
recurrence	B-Application
plot	I-Application
.	O
</s>
<s>
One	O
way	O
to	O
visualize	O
the	O
similarity	O
between	O
two	O
protein	O
or	O
nucleic	O
acid	O
sequences	O
is	O
to	O
use	O
a	O
similarity	O
matrix	O
,	O
known	O
as	O
a	O
dot	B-Application
plot	I-Application
.	O
</s>
<s>
One	O
way	O
of	O
reducing	O
this	O
noise	O
is	O
to	O
only	O
shade	O
runs	O
or	O
'	O
tuples	B-Application
 '	O
of	O
residues	O
,	O
e.g.	O
</s>
<s>
a	O
tuple	B-Application
of	O
3	O
corresponds	O
to	O
three	O
residues	O
in	O
a	O
row	O
.	O
</s>
<s>
Dot	B-Application
plots	I-Application
compare	O
two	O
sequences	O
by	O
organizing	O
one	O
sequence	O
on	O
the	O
x-axis	O
,	O
and	O
another	O
on	O
the	O
y-axis	O
,	O
of	O
a	O
plot	O
.	O
</s>
<s>
Also	O
note	O
,	O
that	O
the	O
direction	O
of	O
the	O
sequences	O
on	O
the	O
axes	O
will	O
determine	O
the	O
direction	O
of	O
the	O
line	O
on	O
the	O
dot	B-Application
plot	I-Application
.	O
</s>
<s>
A	O
feature	O
that	O
will	O
cause	O
a	O
very	O
different	O
result	O
on	O
the	O
dot	B-Application
plot	I-Application
is	O
the	O
presence	O
of	O
low-complexity	O
region/regions	O
.	O
</s>
<s>
These	O
regions	O
are	O
typically	O
found	O
around	O
the	O
diagonal	O
,	O
and	O
may	O
or	O
may	O
not	O
have	O
a	O
square	O
in	O
the	O
middle	O
of	O
the	O
dot	B-Application
plot	I-Application
.	O
</s>
<s>
–	O
Contact	O
analysis	O
of	O
dot	B-Application
plots	I-Application
.	O
</s>
<s>
–	O
Provides	O
a	O
program	O
allowing	O
you	O
to	O
construct	O
a	O
dot	B-Application
plot	I-Application
with	O
your	O
own	O
sequences	O
.	O
</s>
<s>
–	O
Web	O
tool	O
to	O
generate	O
dot	B-Application
plots	I-Application
(	O
and	O
part	O
of	O
the	O
EMBOSS	O
suite	O
)	O
.	O
</s>
<s>
–	O
easy	O
(	O
educational	O
)	O
HTML5	O
tool	O
to	O
generate	O
dot	B-Application
plots	I-Application
from	O
RNA	O
sequences	O
.	O
</s>
<s>
–	O
R	O
package	O
to	O
rapidly	O
generate	O
dot	B-Application
plots	I-Application
as	O
either	O
traditional	O
or	O
ggplot	O
graphics	O
.	O
</s>
<s>
–	O
Stand	O
alone	O
program	O
to	O
generate	O
dot	B-Application
plots	I-Application
.	O
</s>
<s>
–	O
Dot	B-Application
plot	I-Application
tool	O
suitable	O
for	O
even	O
genome	O
scale	O
.	O
</s>
<s>
–	O
An	O
open	O
source	O
Java	O
dot	B-Application
plot	I-Application
program	O
for	O
viruses	O
.	O
</s>
<s>
-	O
Web-based	O
tool	O
to	O
generate	O
(	O
both	O
forward	O
and	O
reverse	O
complement	O
)	O
dot	B-Application
plots	I-Application
from	O
genomic	O
alignments	O
.	O
</s>
<s>
–	O
R	O
package	O
to	O
generate	O
dot	B-Application
plots	I-Application
.	O
</s>
<s>
–	O
Opensource	O
dot	B-Application
plot	I-Application
visualizer	O
.	O
</s>
<s>
In	O
addition	O
to	O
the	O
tools	O
listed	O
above	O
,	O
the	O
NCBI	O
Blast	O
Server	O
at	O
includes	O
Dot	B-Application
Plots	I-Application
in	O
its	O
output	O
.	O
</s>
