<s>
FASTA	B-Application
is	O
a	O
DNA	O
and	O
protein	B-Algorithm
sequence	I-Algorithm
alignment	I-Algorithm
software	O
package	O
first	O
described	O
by	O
David	O
J	O
.	O
Lipman	O
and	O
William	O
R	O
.	O
Pearson	O
in	O
1985	O
.	O
</s>
<s>
Its	O
legacy	O
is	O
the	O
FASTA	B-Application
format	O
which	O
is	O
now	O
ubiquitous	O
in	O
bioinformatics	O
.	O
</s>
<s>
The	O
original	O
FASTA	B-Application
program	O
was	O
designed	O
for	O
protein	O
sequence	O
similarity	O
searching	O
.	O
</s>
<s>
Because	O
of	O
the	O
exponentially	O
expanding	O
genetic	O
information	O
and	O
the	O
limited	O
speed	O
and	O
memory	O
of	O
computers	O
in	O
the	O
1980s	O
heuristic	B-Algorithm
methods	O
were	O
introduced	O
aligning	O
a	O
query	O
sequence	O
to	O
entire	O
data-bases	O
.	O
</s>
<s>
FASTA	B-Application
,	O
published	O
in	O
1987	O
,	O
added	O
the	O
ability	O
to	O
do	O
DNA:DNA	O
searches	O
,	O
translated	O
protein:DNA	O
searches	O
,	O
and	O
also	O
provided	O
a	O
more	O
sophisticated	O
shuffling	O
program	O
for	O
evaluating	O
statistical	O
significance	O
.	O
</s>
<s>
Nowadays	O
,	O
increased	O
computer	O
performance	O
makes	O
it	O
possible	O
to	O
perform	O
searches	O
for	O
local	B-Algorithm
alignment	I-Algorithm
detection	O
in	O
a	O
database	O
using	O
the	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
FASTA	B-Application
is	O
pronounced	O
"	O
fast	O
A	O
"	O
,	O
and	O
stands	O
for	O
"	O
FAST-All	O
"	O
,	O
because	O
it	O
works	O
with	O
any	O
alphabet	O
,	O
an	O
extension	O
of	O
the	O
original	O
"	O
FAST-P	O
"	O
(	O
protein	O
)	O
and	O
"	O
FAST-N	O
"	O
(	O
nucleotide	O
)	O
alignment	O
tools	O
.	O
</s>
<s>
The	O
current	O
FASTA	B-Application
package	O
contains	O
programs	O
for	O
protein:protein	O
,	O
DNA:DNA	O
,	O
protein:translated	O
DNA	O
(	O
with	O
frameshifts	O
)	O
,	O
and	O
ordered	O
or	O
unordered	O
peptide	O
searches	O
.	O
</s>
<s>
Recent	O
versions	O
of	O
the	O
FASTA	B-Application
package	O
include	O
special	O
translated	O
search	O
algorithms	O
that	O
correctly	O
handle	O
frameshift	O
errors	O
(	O
which	O
six-frame-translated	O
searches	O
do	O
not	O
handle	O
very	O
well	O
)	O
when	O
comparing	O
nucleotide	O
to	O
protein	O
sequence	O
data	O
.	O
</s>
<s>
In	O
addition	O
to	O
rapid	O
heuristic	B-Algorithm
search	O
methods	O
,	O
the	O
FASTA	B-Application
package	O
provides	O
SSEARCH	O
,	O
an	O
implementation	O
of	O
the	O
optimal	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
The	O
FASTA	B-Application
package	O
is	O
available	O
from	O
the	O
University	O
of	O
Virginia	O
and	O
the	O
European	O
Bioinformatics	O
Institute	O
.	O
</s>
<s>
The	O
FASTA	B-Application
file	O
format	O
used	O
as	O
input	O
for	O
this	O
software	O
is	O
now	O
largely	O
used	O
by	O
other	O
sequence	O
database	O
search	O
tools	O
(	O
such	O
as	O
BLAST	B-Application
)	O
and	O
sequence	B-Algorithm
alignment	I-Algorithm
programs	O
(	O
Clustal	B-Application
,	O
T-Coffee	B-Application
,	O
etc	O
.	O
</s>
<s>
FASTA	B-Application
takes	O
a	O
given	O
nucleotide	O
or	O
amino	O
acid	O
sequence	O
and	O
searches	O
a	O
corresponding	O
sequence	O
database	O
by	O
using	O
local	O
sequence	B-Algorithm
alignment	I-Algorithm
to	O
find	O
matches	O
of	O
similar	O
database	O
sequences	O
.	O
</s>
<s>
The	O
FASTA	B-Application
program	O
follows	O
a	O
largely	O
heuristic	B-Algorithm
method	O
which	O
contributes	O
to	O
the	O
high	O
speed	O
of	O
its	O
execution	O
.	O
</s>
<s>
It	O
initially	O
observes	O
the	O
pattern	O
of	O
word	O
hits	O
,	O
word-to-word	O
matches	O
of	O
a	O
given	O
length	O
,	O
and	O
marks	O
potential	O
matches	O
before	O
performing	O
a	O
more	O
time-consuming	O
optimized	O
search	O
using	O
a	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
type	O
of	O
algorithm	O
.	O
</s>
<s>
There	O
are	O
some	O
differences	O
between	O
fastn	B-Application
and	O
fastp	B-Application
relating	O
to	O
the	O
type	O
of	O
sequences	O
used	O
but	O
both	O
use	O
four	O
steps	O
and	O
calculate	O
three	O
scores	O
to	O
describe	O
and	O
format	O
the	O
sequence	O
similarity	O
results	O
.	O
</s>
<s>
A	O
carefully	O
calculated	O
cut-off	O
value	O
is	O
thus	O
used	O
to	O
control	O
where	O
this	O
step	O
is	O
implemented	O
,	O
a	O
value	O
that	O
is	O
approximately	O
one	O
standard	B-General_Concept
deviation	I-General_Concept
above	O
the	O
average	O
score	O
expected	O
from	O
unrelated	O
sequences	O
in	O
the	O
library	O
.	O
</s>
<s>
Use	O
a	O
banded	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
algorithm	I-Algorithm
to	O
calculate	O
an	O
optimal	O
score	O
for	O
alignment	O
.	O
</s>
<s>
This	O
step	O
uses	O
a	O
banded	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
algorithm	I-Algorithm
to	O
create	O
an	O
optimised	O
score	O
(	O
opt	O
)	O
for	O
each	O
alignment	O
of	O
query	O
sequence	O
to	O
a	O
database(library )	O
sequence	O
.	O
</s>
<s>
After	O
all	O
sequences	O
are	O
searched	O
the	O
program	O
plots	O
the	O
initial	O
scores	O
of	O
each	O
database	O
sequence	O
in	O
a	O
histogram	B-Algorithm
,	O
and	O
calculates	O
the	O
statistical	O
significance	O
of	O
the	O
"	O
opt	O
"	O
score	O
.	O
</s>
<s>
For	O
protein	O
sequences	O
,	O
the	O
final	O
alignment	O
is	O
produced	O
using	O
a	O
full	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
alignment	O
.	O
</s>
<s>
FASTA	B-Application
can	O
remove	O
complexity	O
regions	O
before	O
aligning	O
the	O
sequences	O
by	O
encoding	O
low	O
complexity	O
regions	O
in	O
lower	O
case	O
and	O
using	O
the	O
-S	O
option	O
.	O
</s>
<s>
However	O
,	O
the	O
BLAST	B-Application
program	O
offers	O
more	O
options	O
for	O
correcting	O
for	O
biased	O
composition	O
statistics	O
.	O
</s>
<s>
Therefore	O
,	O
the	O
program	O
PRSS	O
is	O
added	O
in	O
the	O
FASTA	B-Application
distribution	O
package	O
.	O
</s>
<s>
The	O
FASTA	B-Application
programs	O
find	O
regions	O
of	O
local	O
or	O
global	O
similarity	O
between	O
Protein	O
or	O
DNA	O
sequences	O
,	O
either	O
by	O
searching	O
Protein	O
or	O
DNA	O
databases	O
,	O
or	O
by	O
identifying	O
local	O
duplications	O
within	O
a	O
sequence	O
.	O
</s>
<s>
Like	O
BLAST	B-Application
,	O
FASTA	B-Application
can	O
be	O
used	O
to	O
infer	O
functional	O
and	O
evolutionary	O
relationships	O
between	O
sequences	O
as	O
well	O
as	O
help	O
identify	O
members	O
of	O
gene	O
families	O
.	O
</s>
