<s>
In	O
bioinformatics	O
,	O
a	O
sequence	B-Application
logo	I-Application
is	O
a	O
graphical	O
representation	O
of	O
the	O
sequence	O
conservation	O
of	O
nucleotides	O
(	O
in	O
a	O
strand	O
of	O
DNA/RNA	O
)	O
or	O
amino	O
acids	O
(	O
in	O
protein	O
sequences	O
)	O
.	O
</s>
<s>
A	O
sequence	B-Application
logo	I-Application
is	O
created	O
from	O
a	O
collection	O
of	O
aligned	O
sequences	O
and	O
depicts	O
the	O
consensus	O
sequence	O
and	O
diversity	O
of	O
the	O
sequences	O
.	O
</s>
<s>
Sequence	B-Application
logos	I-Application
are	O
frequently	O
used	O
to	O
depict	O
sequence	O
characteristics	O
such	O
as	O
protein-binding	O
sites	O
in	O
DNA	O
or	O
functional	O
units	O
in	O
proteins	O
.	O
</s>
<s>
A	O
sequence	B-Application
logo	I-Application
consists	O
of	O
a	O
stack	O
of	O
letters	O
at	O
each	O
position	O
.	O
</s>
<s>
To	O
create	O
sequence	B-Application
logos	I-Application
,	O
related	O
DNA	O
,	O
RNA	O
or	O
protein	O
sequences	O
,	O
or	O
DNA	O
sequences	O
that	O
have	O
common	O
conserved	O
binding	O
sites	O
,	O
are	O
aligned	O
so	O
that	O
the	O
most	O
conserved	O
parts	O
create	O
good	O
alignments	O
.	O
</s>
<s>
A	O
sequence	B-Application
logo	I-Application
can	O
then	O
be	O
created	O
from	O
the	O
conserved	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
.	O
</s>
<s>
The	O
sequence	B-Application
logo	I-Application
will	O
show	O
how	O
well	O
residues	O
are	O
conserved	O
at	O
each	O
position	O
:	O
the	O
higher	O
the	O
number	O
of	O
residues	O
,	O
the	O
higher	O
the	O
letters	O
will	O
be	O
,	O
because	O
the	O
better	O
the	O
conservation	O
is	O
at	O
that	O
position	O
.	O
</s>
<s>
Sequence	B-Application
logos	I-Application
can	O
be	O
used	O
to	O
represent	O
conserved	O
DNA	O
binding	O
sites	O
,	O
where	O
transcription	O
factors	O
bind	O
.	O
</s>
<s>
A	O
consensus	O
logo	O
is	O
a	O
simplified	O
variation	O
of	O
a	O
sequence	B-Application
logo	I-Application
that	O
can	O
be	O
embedded	O
in	O
text	O
format	O
.	O
</s>
<s>
The	O
main	O
,	O
and	O
obvious	O
,	O
advantage	O
of	O
consensus	O
logos	O
over	O
sequence	B-Application
logos	I-Application
is	O
their	O
ability	O
to	O
be	O
embedded	O
as	O
text	O
in	O
any	O
Rich	O
Text	O
Format	O
supporting	O
editor/viewer	O
and	O
,	O
therefore	O
,	O
in	O
scientific	O
manuscripts	O
.	O
</s>
<s>
As	O
described	O
above	O
,	O
the	O
consensus	O
logo	O
is	O
a	O
cross	O
between	O
sequence	B-Application
logos	I-Application
and	O
consensus	O
sequences	O
.	O
</s>
<s>
As	O
a	O
result	O
,	O
compared	O
to	O
a	O
sequence	B-Application
logo	I-Application
,	O
the	O
consensus	O
logo	O
omits	O
information	O
(	O
the	O
relative	O
contribution	O
of	O
each	O
character	O
to	O
the	O
conservation	O
of	O
that	O
position	O
in	O
the	O
motif/alignment	O
)	O
.	O
</s>
<s>
Hence	O
,	O
a	O
sequence	B-Application
logo	I-Application
should	O
be	O
used	O
preferentially	O
whenever	O
possible	O
.	O
</s>
<s>
That	O
being	O
said	O
,	O
the	O
need	O
to	O
include	O
graphic	O
figures	O
in	O
order	O
to	O
display	O
sequence	B-Application
logos	I-Application
has	O
perpetuated	O
the	O
use	O
of	O
consensus	O
sequences	O
in	O
scientific	O
manuscripts	O
,	O
even	O
though	O
they	O
fail	O
to	O
convey	O
information	O
on	O
both	O
conservation	O
and	O
frequency	O
.	O
</s>
<s>
In	O
an	O
HMM	O
sequence	B-Application
logo	I-Application
used	O
by	O
Pfam	O
,	O
three	O
rows	O
are	O
added	O
to	O
indicate	O
the	O
frequencies	O
of	O
occupancy	O
(	O
presence	O
)	O
and	O
insertion	O
,	O
as	O
well	O
as	O
the	O
expected	O
insertion	O
length	O
.	O
</s>
