<s>
In	O
computer	B-General_Concept
science	I-General_Concept
,	O
a	O
compressed	B-Algorithm
suffix	I-Algorithm
array	I-Algorithm
is	O
a	O
compressed	B-Data_Structure
data	I-Data_Structure
structure	I-Data_Structure
for	O
pattern	B-Language
matching	I-Language
.	O
</s>
<s>
Compressed	B-Algorithm
suffix	I-Algorithm
arrays	I-Algorithm
are	O
a	O
general	O
class	O
of	O
data	B-General_Concept
structure	I-General_Concept
that	O
improve	O
on	O
the	O
suffix	B-Algorithm
array	I-Algorithm
.	O
</s>
<s>
These	O
data	B-General_Concept
structures	I-General_Concept
enable	O
quick	O
search	O
for	O
an	O
arbitrary	O
string	O
with	O
a	O
comparatively	O
small	O
index	O
.	O
</s>
<s>
Given	O
a	O
text	O
T	O
of	O
n	O
characters	O
from	O
an	O
alphabet	O
Σ	O
,	O
a	O
compressed	B-Algorithm
suffix	I-Algorithm
array	I-Algorithm
supports	O
searching	O
for	O
arbitrary	O
patterns	O
in	O
T	O
.	O
For	O
an	O
input	O
pattern	O
P	O
of	O
m	O
characters	O
,	O
the	O
search	O
time	O
is	O
typically	O
O(m )	O
or	O
O( m	O
+	O
log(n )	O
)	O
.	O
</s>
<s>
The	O
space	O
used	O
is	O
typically	O
,	O
where	O
is	O
the	O
k-th	O
order	O
empirical	O
entropy	O
of	O
the	O
text	O
T	O
.	O
The	O
time	O
and	O
space	O
to	O
construct	O
a	O
compressed	B-Algorithm
suffix	I-Algorithm
array	I-Algorithm
are	O
normally	O
.	O
</s>
<s>
The	O
original	O
instantiation	O
of	O
the	O
compressed	B-Algorithm
suffix	I-Algorithm
array	I-Algorithm
solved	O
a	O
long-standing	O
open	O
problem	O
by	O
showing	O
that	O
fast	O
pattern	B-Language
matching	I-Language
was	O
possible	O
using	O
only	O
a	O
linear-space	O
data	B-General_Concept
structure	I-General_Concept
,	O
namely	O
,	O
one	O
proportional	O
to	O
the	O
size	O
of	O
the	O
text	O
T	O
,	O
which	O
takes	O
bits	O
.	O
</s>
<s>
The	O
conventional	O
suffix	B-Algorithm
array	I-Algorithm
and	O
suffix	O
tree	O
use	O
bits	O
,	O
which	O
is	O
substantially	O
larger	O
.	O
</s>
<s>
The	O
basis	O
for	O
the	O
data	B-General_Concept
structure	I-General_Concept
is	O
a	O
recursive	O
decomposition	O
using	O
the	O
"	O
neighbor	O
function	O
,	O
"	O
which	O
allows	O
a	O
suffix	B-Algorithm
array	I-Algorithm
to	O
be	O
represented	O
by	O
one	O
of	O
half	O
its	O
length	O
.	O
</s>
<s>
The	O
construction	O
is	O
repeated	O
multiple	O
times	O
until	O
the	O
resulting	O
suffix	B-Algorithm
array	I-Algorithm
uses	O
a	O
linear	O
number	O
of	O
bits	O
.	O
</s>
<s>
The	O
space	O
bound	O
was	O
further	O
improved	O
achieving	O
the	O
ultimate	O
goal	O
of	O
higher-order	O
entropy	O
;	O
the	O
compression	O
is	O
obtained	O
by	O
partitioning	O
the	O
neighbor	O
function	O
by	O
high-order	O
contexts	O
,	O
and	O
compressing	O
each	O
partition	O
with	O
a	O
wavelet	B-Data_Structure
tree	I-Data_Structure
.	O
</s>
<s>
The	O
space	O
usage	O
is	O
extremely	O
competitive	O
in	O
practice	O
with	O
other	O
state-of-the-art	O
compressors	O
,	O
and	O
it	O
also	O
supports	O
fast	O
pattern	B-Language
matching	I-Language
.	O
</s>
<s>
The	O
memory	O
accesses	O
made	O
by	O
compressed	B-Algorithm
suffix	I-Algorithm
arrays	I-Algorithm
and	O
other	O
compressed	B-Data_Structure
data	I-Data_Structure
structures	I-Data_Structure
for	O
pattern	B-Language
matching	I-Language
are	O
typically	O
not	O
localized	O
,	O
and	O
thus	O
these	O
data	B-General_Concept
structures	I-General_Concept
have	O
been	O
notoriously	O
hard	O
to	O
design	O
efficiently	O
for	O
use	O
in	O
external	O
memory	O
.	O
</s>
<s>
Recent	O
progress	O
using	O
geometric	O
duality	O
takes	O
advantage	O
of	O
the	O
block	O
access	O
provided	O
by	O
disks	O
to	O
speed	O
up	O
the	O
I/O	O
time	O
significantly	O
In	O
addition	O
,	O
potentially	O
practical	O
search	O
performance	O
for	O
a	O
compressed	B-Algorithm
suffix	I-Algorithm
array	I-Algorithm
in	O
external-memory	O
has	O
been	O
demonstrated	O
.	O
</s>
<s>
There	O
are	O
several	O
open	O
source	O
implementations	O
of	O
compressed	B-Algorithm
suffix	I-Algorithm
arrays	I-Algorithm
available	O
(	O
see	O
External	O
Links	O
below	O
)	O
.	O
</s>
<s>
Bowtie	O
and	O
Bowtie2	O
are	O
open-source	O
compressed	B-Algorithm
suffix	I-Algorithm
array	I-Algorithm
implementations	O
of	O
read	B-Algorithm
alignment	I-Algorithm
for	O
use	O
in	O
bioinformatics	O
.	O
</s>
<s>
The	O
Succinct	O
Data	B-General_Concept
Structure	I-General_Concept
Library	O
(	O
SDSL	O
)	O
is	O
a	O
library	O
containing	O
a	O
variety	O
of	O
compressed	B-Data_Structure
data	I-Data_Structure
structures	I-Data_Structure
including	O
compressed	B-Algorithm
suffix	I-Algorithm
arrays	I-Algorithm
.	O
</s>
<s>
FEMTO	O
is	O
an	O
implementation	O
of	O
compressed	B-Algorithm
suffix	I-Algorithm
arrays	I-Algorithm
for	O
external	O
memory	O
.	O
</s>
<s>
In	O
addition	O
,	O
a	O
variety	O
of	O
implementations	O
,	O
including	O
the	O
original	O
FM-index	B-Algorithm
implementations	O
,	O
are	O
available	O
from	O
the	O
Pizza	O
&	O
Chili	O
Website	O
(	O
see	O
external	O
links	O
)	O
.	O
</s>
