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s
eq
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ce
s
d
atab
ase
[1
-
4]
.
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DN
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-
8]
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[9
-
10]
.
T
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atio
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r
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Nee
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u
n
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Fig
u
r
e
3
.
E
x
a
m
p
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o
f
DN
A
s
e
q
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en
ce
ce
ll i
n
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izatio
n
S1
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--
NC
HE
S
S2
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--
NC
HE
S
2.
RE
S
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M
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T
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D
As
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h
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m
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Me
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[
2
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o
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ith
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u
r
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6
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P
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RE
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L
T
S AN
D
AN
AL
Y
SI
S
T
h
is
s
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tio
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s
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h
e
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tat
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n
ce
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o
r
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m
s
;
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it
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P
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d
Gr
ap
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ics
P
r
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ce
s
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g
Un
it
(
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U)
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h
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s
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e
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th
o
f
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A
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eq
u
e
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ce
s
ac
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s
as a
b
en
c
h
m
ar
k
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n
th
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s
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m
p
ar
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n
.
3
.
1
.
Da
t
a
Co
llect
io
n F
ro
m
B
a
s
e
P
a
ir
Sequ
ence
s
I
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d
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f
r
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m
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eth
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to
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m
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h
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s
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m
ilar
s
ize
o
f
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at
a
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1
s
t
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eq
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n
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2
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eq
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ce
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h
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llectio
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at
a
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d
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m
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f
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ith
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e
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r
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m
1
to
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0
0
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th
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s
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e
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ce
.
T
ab
le
1
.
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it
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-
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ater
m
a
n
GP
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m
o
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el
T
ab
le
2
.
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h
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ater
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n
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m
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el
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a
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p
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T
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me
(
ms)
1
0
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0
1
5
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0
1
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0
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5
4
0
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0
3
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ased
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ase
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ased
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ce
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o
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ith
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th
o
f
1
3
8
,
1
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2
0
1
,
2
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2
6
0
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d
2
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,
r
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elate
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f
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k
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al
p
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lem
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ith
m
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s
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b
y
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r
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al
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to
s
o
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t
h
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r
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lem
,
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ea
s
y
to
b
r
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k
it
d
o
w
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to
s
m
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ar
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it
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y
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it
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eq
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en
tial
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e
r
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ti
m
e
ta
k
es
to
s
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t
h
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p
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lem
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t s
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4.
CO
NCLU
SI
O
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I
n
t
h
is
p
ap
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w
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d
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s
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s
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th
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p
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e
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A
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eq
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t
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m
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ater
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al
P
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s
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it
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ap
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r
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it
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et
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ase
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g
o
r
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u
s
in
g
NVI
DI
A
C
UD
A
h
as
s
u
cc
es
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u
ll
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v
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t
h
e
b
est
r
es
u
lt
co
m
p
ar
ed
to
t
h
e
C
P
U,
w
h
ic
h
s
h
o
w
,
t
h
e
ad
v
an
ta
g
e
o
f
t
h
e
p
ar
allelis
m
o
f
t
h
e
GP
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n
b
r
in
g
o
u
t
t
h
e
h
ig
h
p
er
f
o
r
m
a
n
ce
o
f
SW
al
g
o
r
ith
m
.
Ot
h
er
t
h
an
u
s
e
f
o
r
s
eq
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en
ce
alig
n
m
en
t
s
s
u
c
h
as
DN
A
an
d
p
r
o
tein
,
th
e
SW
alg
o
r
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m
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ca
n
b
e
ap
p
lied
as
a
s
p
a
m
f
ilter
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r
p
lag
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s
m
d
etec
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n
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a
n
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r
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ir
ed
t
h
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n
ee
d
f
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m
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.
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o
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er
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w
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h
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r
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o
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i
m
p
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o
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in
t
h
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f
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[1
]
Kim
KB,
Yu
DH
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.
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sh
ip
De
g
re
e
T
h
e
P
r
o
p
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se
d
A
lg
o
rit
h
m
f
o
r
DN
A
S
e
q
u
e
n
c
e
A
n
a
ly
sis"
.
2
0
1
2
;
3
5
2
-
3
5
4
.
[2
]
Ju
n
id
S
A
M
A
l,
T
a
h
ir
NM,
M
a
ji
d
ZA
,
Os
m
a
n
F
N,
S
h
a
rif
f
KK
M
.
"
Co
m
p
a
ra
ti
v
e
stu
d
y
f
o
r
DN
A
d
a
ta
m
in
i
m
iza
ti
o
n
tec
h
n
iq
u
e
o
n
F
P
G
A"
.
ICIAS
2
0
1
2
-
2
0
1
2
4
th
I
n
t
C
o
n
f
In
tell
Ad
v
S
y
st
A
Co
n
f
W
o
rl
d
En
g
S
c
i
T
e
c
h
n
o
l
C
o
n
g
r
-
Co
n
f
Pro
c
.
2
0
1
2
;2
:7
6
5
-
7
6
7
.
[3
]
Ju
n
id
S
a
.
M
A
l,
Ha
ro
n
M
a
.
,
M
a
ji
d
ZA
,
Ha
li
m
a
.
K,
Os
m
a
n
F
N,
Ha
sh
im
H.
"
De
v
e
lo
p
m
e
n
t
o
f
No
v
e
l
Da
t
a
Co
m
p
re
ss
io
n
T
e
c
h
n
iq
u
e
f
o
r
A
c
c
e
lera
te
DN
A
S
e
q
u
e
n
c
e
A
li
g
n
m
e
n
t
Ba
se
d
o
n
S
m
it
h
–
W
a
ter
m
a
n
Alg
o
rit
h
m
"
.
2
0
0
9
T
h
ird
UK
S
im
E
u
r S
y
mp
Co
mp
u
t
M
o
d
e
l
S
im
u
l
.
2
0
0
9
;
1
8
1
-
1
8
6
.
[4
]
A
l
Ju
n
id
S
A
M
,
Ha
ro
n
M
A
,
Ab
d
M
a
ji
d
Z,
e
t
a
l.
"
Op
ti
m
iz
a
ti
o
n
o
f
DN
A
se
q
u
e
n
c
e
s
d
a
ta
f
o
r
a
c
c
e
ler
a
te
DN
A
se
q
u
e
n
c
e
s
a
li
g
n
m
e
n
t
o
n
F
P
G
A"
.
AM
S
2
0
1
0
Asia
M
o
d
e
l
S
y
mp
2
0
1
0
-
4
th
I
n
t
Co
n
f
M
a
th
M
o
d
e
l
Co
mp
u
t
S
imu
l
.
2
0
1
0
;
2
3
1
-
2
3
6
.
[5
]
S
h
u
JJ
,
Yo
n
g
KY
,
Ch
a
n
W
K.
"
A
n
i
m
p
ro
v
e
d
sc
o
r
in
g
m
a
tri
x
f
o
r
m
u
lt
ip
le
se
q
u
e
n
c
e
a
li
g
n
m
e
n
t"
.
M
a
th
Pro
b
l
En
g
.
2
0
1
2
;
2
0
1
2
.
[6
]
Kh
a
led
H,
G
o
h
a
ry
R
El
,
Ba
d
r
NL
,
F
a
h
e
e
m
HM.
"
A
c
c
e
lera
ti
n
g
p
a
irw
ise
D
N
A
S
e
q
u
e
n
c
e
A
li
g
n
m
e
n
t
u
sin
g
th
e
CUD
A
c
o
m
p
a
ti
b
le G
P
U"
.
In
t
J
Co
m
p
u
t
Ap
p
l
.
2
0
1
3
;8
4
(1
):2
5
-
3
1
.
[7
]
Ne
v
e
s
N,
S
e
b
a
stiao
N,
P
a
tri
c
i
o
A
,
e
t
a
l.
"
Bio
Blaz
e
:
M
u
lt
i
-
c
o
re
S
I
M
D
A
S
IP
f
o
r
DN
A
se
q
u
e
n
c
e
a
li
g
n
m
e
n
t"
.
Pro
c
In
t
Co
n
f
Ap
p
l
S
y
st
Arc
h
it
Pr
o
c
e
ss
.
2
0
1
3
;
2
4
1
-
2
4
4
.
[8
]
Ch
a
k
ra
b
a
rti
T
,
Be
n
g
a
l
W
.
"
D
N
A
M
u
lt
i
p
le
S
e
q
u
e
n
c
e
A
li
g
n
m
e
n
t
b
y
a
Hid
d
e
n
M
a
rk
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v
M
o
d
e
l
a
n
d
F
u
z
z
y
L
e
v
e
n
s
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tein
Dista
n
c
e
b
a
se
d
G
e
n
e
ti
c
A
lg
o
rit
h
m
"
.
2
0
1
3
;7
3
(1
6
):2
6
-
3
0
.
[9
]
Zh
a
n
g
J,
Ya
n
g
C.
"
DN
A
se
q
u
e
n
c
e
re
c
o
g
n
it
io
n
b
a
se
d
o
n
th
e
M
a
rk
o
v
m
o
d
e
l"
.
2
0
1
3
6
t
h
In
t
Co
n
f
Bi
o
me
d
E
n
g
In
fo
rm
a
t
ics
.
2
0
1
3
;(Bm
e
i):
5
3
6
-
5
4
0
.
[1
0
]
Ha
li
m
A
K,
Ha
ru
n
M
H,
M
o
h
a
m
e
d
S
,
M
a
ji
d
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,
M
a
n
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r
M
A
,
Ju
n
id
S
A
M
A
.
"
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o
w
p
o
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stu
d
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o
n
trac
e
b
a
c
k
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n
d
re
c
o
n
stru
c
ti
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n
m
o
d
u
les
f
o
r
DN
A
se
q
u
e
n
c
e
s
a
li
g
n
m
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t
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c
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to
r"
.
Pro
c
-
2
0
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2
1
4
t
h
In
t
C
o
n
f
M
o
d
e
l
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ti
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n
,
UKS
im
2
0
1
2
.
2
0
1
2
;(
1
):1
1
7
-
1
2
5
.
[1
1
]
A
b
d
u
l
S
,
A
l
M
,
M
a
ji
d
ZA
,
Ha
li
m
A
K.
"
De
v
e
lo
p
m
e
n
t
o
f
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a
S
e
q
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e
n
c
i
n
g
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ler
a
to
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se
d
o
n
S
m
it
h
Wate
r
m
a
n
A
l
g
o
rit
h
m
W
it
h
He
u
risti
c
Div
id
e
a
n
d
Co
n
q
u
e
r
T
e
c
h
n
iq
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e
f
o
r
F
p
g
a
Im
p
le
m
e
n
tatio
n
"
.
2
0
0
8
:
9
9
4
-
9
9
6
.
[1
2
]
A
l
Ju
n
id
S
A
M
,
M
d
T
a
h
ir
N,
A
b
d
M
a
ji
d
Z,
Oth
m
a
n
Z,
M
o
h
d
S
h
a
ri
ff
KK
.
"
R
e
d
u
c
in
g
m
e
m
o
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y
c
o
m
p
lex
it
y
u
sin
g
d
a
ta
m
in
i
m
iza
ti
o
n
tec
h
n
i
q
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o
n
F
P
G
A"
.
20
1
2
I
n
t
C
o
n
f
C
o
mp
u
t
I
n
f
S
c
i
.
2
0
1
2
:
4
3
1
-
4
3
4
.
[1
3
]
Ra
z
ip
M
IM
,
J
u
n
i
d
S
A
M
A
l,
Ha
li
m
A
K,
M
a
ji
d
ZA
.
"
S
e
q
u
e
n
c
e
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li
g
n
m
e
n
t
u
sin
g
s
y
sto
li
c
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rra
y
f
o
r
a
n
a
c
c
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to
r"
.
2
0
1
4
IE
EE
8
th
I
n
t
Po
we
r E
n
g
O
p
ti
m Co
n
f
.
2
0
1
4
;(
M
a
rc
h
):6
6
3
-
6
6
5
.
[1
4
]
Ju
n
id
S
A
M
A
l,
T
a
h
ir
NM,
M
a
ji
d
ZA
,
Ha
li
m
A
K,
S
h
a
riff
KK
M
.
"
Im
p
ro
v
e
d
d
a
ta
m
in
i
m
iza
ti
o
n
tec
h
n
iq
u
e
i
n
re
d
u
c
in
g
m
e
m
o
r
y
sp
a
c
e
c
o
m
p
lex
it
y
f
o
r
DN
A
lo
c
a
l
a
li
g
n
m
e
n
t
a
c
c
e
l
e
ra
to
r
a
p
p
li
c
a
ti
o
n
"
.
I
S
CAIE
2
0
1
2
-
2
0
1
2
IEE
E
S
y
mp
Co
mp
u
t
Ap
p
l
I
n
d
El
e
c
tro
n
.
2
0
1
2
;
(Isc
a
ie):1
5
3
-
1
5
6
.
[1
5
]
Ru
c
c
i
E,
G
a
rc
i
a
C,
Bo
tella
G
,
G
iu
sti
A
De
,
N
a
io
u
f
M
,
P
riet
o
-
M
a
ti
a
s
M
.
"
S
m
it
h
-
Wate
r
m
a
n
P
ro
tein
S
e
a
rc
h
w
it
h
Op
e
n
CL
o
n
a
n
F
P
G
A"
.
Pro
c
-
1
4
th
IEE
E
In
t
Co
n
f
T
r
u
st S
e
c
u
r
Priv Co
mp
u
t
Co
mm
u
n
T
ru
st
2
0
1
5
.
2
0
1
5
;
3
:2
0
8
-
2
1
3
.
[1
6
]
Ca
sa
le
-
b
ru
n
e
t
S
,
Be
z
a
ti
E,
M
a
tt
a
v
e
ll
i
M
.
"
De
sig
n
sp
a
c
e
e
x
p
lo
ra
ti
o
n
o
f
d
a
taf
lo
w
-
b
a
se
d
S
m
it
h
-
Wate
r
m
a
n
F
P
G
A
im
p
le
m
e
n
tatio
n
s"
.
[1
7
]
Zah
id
S
K,
Ha
sa
n
L
,
Kh
a
n
AA
,
U
ll
a
h
S
.
"
A
n
o
v
e
l
stru
c
tu
re
o
f
th
e
S
m
it
h
-
W
a
ter
m
a
n
A
lg
o
rit
h
m
f
o
r
e
ff
icie
n
t
se
q
u
e
n
c
e
a
li
g
n
m
e
n
t
".
2
0
1
5
3
rd
I
n
t
C
o
n
f
Di
g
it
I
n
fo
rm
a
ti
o
n
,
Ne
tw
o
rk
in
g
,
W
ire
l
Co
mm
u
n
DINW
C
2
0
1
5
.
2
0
1
5
:6
-
9.
[1
8
]
Ca
u
sa
p
ru
n
o
G
,
Urg
e
se
G
,
V
a
c
c
a
M
,
G
ra
z
ian
o
M
.
"
P
ro
tei
n
A
li
g
n
m
e
n
t
S
y
sto
li
c
A
rra
y
T
h
ro
u
g
h
p
u
t
Op
ti
m
iza
ti
o
n
"
.
T
v
lsi
.
2
0
1
5
;2
3
(1
):
6
8
-
7
7
.
[1
9
]
Ju
n
id
S
A
M
A
l,
Id
ro
s
M
F
M
,
Ra
z
a
k
A
H
A
,
Os
m
a
n
F
N,
Tah
ir
NM.
"
P
a
ra
ll
e
l
p
r
o
c
e
ss
in
g
c
e
ll
sc
o
re
d
e
si
g
n
o
f
li
n
e
a
r
g
a
p
p
e
n
a
lt
y
s
m
it
h
-
w
a
ter
m
a
n
a
lg
o
rit
h
m
"
.
Pro
c
-
2
0
1
7
IEE
E
1
3
th
I
n
t
Co
ll
o
q
S
ig
n
a
l
Pro
c
e
ss
it
s
Ap
p
l
CS
P
A
2
0
1
7
.
2
0
1
7
;(M
a
rc
h
)
:2
9
9
-
3
0
2
.
[2
0
]
Ha
sa
n
L
,
A
l
-
A
rs
Z.
"
A
n
Ov
e
rv
ie
w
o
f
Ha
rd
w
a
re
-
Ba
se
d
Ac
c
e
ler
a
ti
o
n
o
f
Bio
lo
g
ica
l
S
e
q
u
e
n
c
e
A
li
g
n
m
e
n
t"
.
Co
mp
u
t
Bi
o
l
A
p
p
l
.
2
0
1
1
.
h
tt
p
:/
/cd
n
.
in
tec
h
o
p
e
n
.
c
o
m
/p
d
f
s/1
8
9
9
7
/In
T
e
c
h
A
n
_
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v
e
rv
ie
w
_
o
f
_
h
a
rd
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re
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b
a
se
d
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c
c
e
ler
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ti
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n
_
o
f
_
b
io
lo
g
ica
l_
se
q
u
e
n
c
e
_
a
li
g
n
m
e
n
t.
p
d
f
.
[2
1
]
Bu
sta
m
a
m
A
,
A
rd
a
n
e
s
w
a
ri
G
,
Les
tari
D.
"
I
m
p
le
m
e
n
tatio
n
o
f
CUD
A
G
P
U
-
Ba
se
d
P
a
ra
ll
e
l
Co
m
p
u
ti
n
g
o
n
S
m
it
h
-
W
a
ter
m
a
n
A
l
g
o
rit
h
m
to
S
e
q
u
e
n
c
e
Da
tab
a
se
S
e
a
rc
h
e
s
"
.
2
0
1
3
;9
7
8
-
9
7
9
.
[2
2
]
Ch
e
n
g
J,
G
ro
ss
m
a
n
M
,
M
c
k
e
rc
h
e
r
T
.
P
ROF
ES
S
IONAL
CUD
A
C
P
ro
g
ra
mm
in
g
.
2
0
1
4
.
[23]
Ha
sa
n
L
,
K
e
n
ti
e
M
,
A
l
-
A
rs
Z
.
"
DO
P
A
:
G
P
U
-
b
a
se
d
p
r
o
tein
a
li
g
n
m
e
n
t
u
sin
g
d
a
tab
a
se
a
n
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