<s>
In	O
computer	B-General_Concept
science	I-General_Concept
,	O
an	O
FM-index	B-Algorithm
is	O
a	O
compressed	O
full-text	O
substring	B-Algorithm
index	I-Algorithm
based	O
on	O
the	O
Burrows	B-Algorithm
–	I-Algorithm
Wheeler	I-Algorithm
transform	I-Algorithm
,	O
with	O
some	O
similarities	O
to	O
the	O
suffix	B-Algorithm
array	I-Algorithm
.	O
</s>
<s>
The	O
query	O
time	O
,	O
as	O
well	O
as	O
the	O
required	O
storage	B-Language
space	I-Language
,	O
has	O
a	O
sublinear	O
complexity	O
with	O
respect	O
to	O
the	O
size	O
of	O
the	O
input	O
data	O
.	O
</s>
<s>
The	O
original	O
authors	O
have	O
devised	O
improvements	O
to	O
their	O
original	O
approach	O
and	O
dubbed	O
it	O
"	O
FM-Index	B-Algorithm
version	O
2	O
"	O
.	O
</s>
<s>
A	O
further	O
improvement	O
,	O
the	O
alphabet-friendly	O
FM-index	B-Algorithm
,	O
combines	O
the	O
use	O
of	O
compression	O
boosting	O
and	O
wavelet	B-Data_Structure
trees	I-Data_Structure
to	O
significantly	O
reduce	O
the	O
space	O
usage	O
for	O
large	O
alphabets	O
.	O
</s>
<s>
The	O
FM-index	B-Algorithm
has	O
found	O
use	O
in	O
,	O
among	O
other	O
places	O
,	O
bioinformatics	O
.	O
</s>
<s>
When	O
the	O
FM-index	B-Algorithm
was	O
introduced	O
,	O
there	O
were	O
several	O
suggested	O
solutions	O
that	O
were	O
based	O
on	O
traditional	O
compression	O
methods	O
and	O
tried	O
to	O
solve	O
the	O
compressed	O
matching	O
problem	O
.	O
</s>
<s>
In	O
contrast	O
,	O
the	O
FM-index	B-Algorithm
is	O
a	O
compressed	O
self-index	O
,	O
which	O
means	O
that	O
it	O
compresses	O
the	O
data	O
and	O
indexes	O
it	O
at	O
the	O
same	O
time	O
.	O
</s>
<s>
An	O
FM-index	B-Algorithm
is	O
created	O
by	O
first	O
taking	O
the	O
Burrows	B-Algorithm
–	I-Algorithm
Wheeler	I-Algorithm
transform	I-Algorithm
(	O
BWT	O
)	O
of	O
the	O
input	O
text	O
.	O
</s>
<s>
The	O
BWT	O
in	O
itself	O
allows	O
for	O
some	O
compression	O
with	O
,	O
for	O
instance	O
,	O
move	B-Algorithm
to	I-Algorithm
front	I-Algorithm
and	O
Huffman	B-General_Concept
encoding	I-General_Concept
,	O
but	O
the	O
transform	O
has	O
even	O
more	O
uses	O
.	O
</s>
<s>
The	O
rows	O
in	O
the	O
matrix	O
are	O
essentially	O
the	O
sorted	O
suffixes	O
of	O
the	O
text	O
and	O
the	O
first	O
column	O
F	O
of	O
the	O
matrix	O
shares	O
similarities	O
with	O
suffix	B-Algorithm
arrays	I-Algorithm
.	O
</s>
<s>
How	O
the	O
suffix	B-Algorithm
array	I-Algorithm
relates	O
to	O
the	O
BWT	O
lies	O
at	O
the	O
heart	O
of	O
the	O
FM-index	B-Algorithm
.	O
</s>
