<s>
In	O
bioinformatics	O
,	O
BLAST	B-Application
(	O
basic	B-Application
local	I-Application
alignment	I-Application
search	I-Application
tool	I-Application
)	O
is	O
an	O
algorithm	O
and	O
program	O
for	O
comparing	O
primary	O
biological	O
sequence	O
information	O
,	O
such	O
as	O
the	O
amino-acid	O
sequences	O
of	O
proteins	O
or	O
the	O
nucleotides	O
of	O
DNA	O
and/or	O
RNA	O
sequences	O
.	O
</s>
<s>
A	O
BLAST	B-Application
search	O
enables	O
a	O
researcher	O
to	O
compare	O
a	O
subject	O
protein	O
or	O
nucleotide	O
sequence	O
(	O
called	O
a	O
query	O
)	O
with	O
a	O
library	O
or	O
database	O
of	O
sequences	O
,	O
and	O
identify	O
database	O
sequences	O
that	O
resemble	O
alphabet	O
above	O
a	O
certain	O
threshold	O
.	O
</s>
<s>
For	O
example	O
,	O
following	O
the	O
discovery	O
of	O
a	O
previously	O
unknown	O
gene	O
in	O
the	O
mouse	O
,	O
a	O
scientist	O
will	O
typically	O
perform	O
a	O
BLAST	B-Application
search	O
of	O
the	O
human	O
genome	O
to	O
see	O
if	O
humans	O
carry	O
a	O
similar	O
gene	O
;	O
BLAST	B-Application
will	O
identify	O
sequences	O
in	O
the	O
human	O
genome	O
that	O
resemble	O
the	O
mouse	O
gene	O
based	O
on	O
similarity	O
of	O
sequence	O
.	O
</s>
<s>
BLAST	B-Application
,	O
which	O
The	O
New	O
York	O
Times	O
called	O
the	O
Google	O
of	O
biological	O
research	O
,	O
is	O
one	O
of	O
the	O
most	O
widely	O
used	O
bioinformatics	O
programs	O
for	O
sequence	O
searching	O
.	O
</s>
<s>
The	O
heuristic	B-Algorithm
algorithm	I-Algorithm
it	O
uses	O
is	O
much	O
faster	O
than	O
other	O
approaches	O
,	O
such	O
as	O
calculating	O
an	O
optimal	O
alignment	O
.	O
</s>
<s>
Before	O
BLAST	B-Application
,	O
FASTA	B-Application
was	O
developed	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>
BLAST	B-Application
came	O
from	O
the	O
1990	O
stochastic	O
model	O
of	O
Samuel	O
Karlin	O
and	O
Stephen	O
Altschul	O
They	O
proposed	O
"	O
a	O
method	O
for	O
estimating	O
similarities	O
between	O
the	O
known	O
DNA	O
sequence	O
of	O
one	O
organism	O
with	O
that	O
of	O
another	O
"	O
,	O
and	O
their	O
work	O
has	O
been	O
described	O
as	O
"	O
the	O
statistical	O
foundation	O
for	O
BLAST.	O
"	O
</s>
<s>
Subsequently	O
,	O
Altschul	O
,	O
along	O
with	O
Warren	O
Gish	O
,	O
Webb	O
Miller	O
,	O
Eugene	O
Myers	O
,	O
and	O
David	O
J	O
.	O
Lipman	O
at	O
the	O
National	O
Institutes	O
of	O
Health	O
designed	O
the	O
BLAST	B-Application
algorithm	O
,	O
which	O
was	O
published	O
in	O
the	O
Journal	O
of	O
Molecular	O
Biology	O
in	O
1990	O
and	O
cited	O
over	O
75,000	O
times	O
.	O
</s>
<s>
While	O
BLAST	B-Application
is	O
faster	O
than	O
any	O
Smith-Waterman	B-Algorithm
implementation	O
for	O
most	O
cases	O
,	O
it	O
cannot	O
"	O
guarantee	O
the	O
optimal	O
alignments	O
of	O
the	O
query	O
and	O
database	O
sequences	O
"	O
as	O
Smith-Waterman	B-Algorithm
algorithm	I-Algorithm
does	O
.	O
</s>
<s>
The	O
optimality	O
of	O
Smith-Waterman	B-Algorithm
"	O
ensured	O
the	O
best	O
performance	O
on	O
accuracy	O
and	O
the	O
most	O
precise	O
results	O
"	O
at	O
the	O
expense	O
of	O
time	O
and	O
computer	O
power	O
.	O
</s>
<s>
BLAST	B-Application
is	O
more	O
time-efficient	O
than	O
FASTA	B-Application
by	O
searching	O
only	O
for	O
the	O
more	O
significant	O
patterns	O
in	O
the	O
sequences	O
,	O
yet	O
with	O
comparative	O
sensitivity	O
.	O
</s>
<s>
This	O
could	O
be	O
further	O
realized	O
by	O
understanding	O
the	O
algorithm	O
of	O
BLAST	B-Application
introduced	O
below	O
.	O
</s>
<s>
Examples	O
of	O
other	O
questions	O
that	O
researchers	O
use	O
BLAST	B-Application
to	O
answer	O
are	O
:	O
</s>
<s>
BLAST	B-Application
is	O
also	O
often	O
used	O
as	O
part	O
of	O
other	O
algorithms	O
that	O
require	O
approximate	O
sequence	O
matching	O
.	O
</s>
<s>
BLAST	B-Application
is	O
available	O
on	O
the	O
web	O
on	O
the	O
NCBI	O
website	O
.	O
</s>
<s>
Different	O
types	O
of	O
BLASTs	B-Application
are	O
available	O
according	O
to	O
the	O
query	O
sequences	O
and	O
the	O
target	O
databases	O
.	O
</s>
<s>
Alternative	O
implementations	O
include	O
AB-BLAST	O
(	O
formerly	O
known	O
as	O
WU-BLAST	O
)	O
,	O
FSA-BLAST	O
(	O
last	O
updated	O
in	O
2006	O
)	O
,	O
and	O
ScalaBLAST	O
.	O
</s>
<s>
Input	O
sequences	O
(	O
in	O
FASTA	B-Application
or	O
Genbank	O
format	O
)	O
,	O
database	O
to	O
search	O
and	O
other	O
optional	O
parameters	O
such	O
as	O
scoring	O
matrix	O
.	O
</s>
<s>
BLAST	B-Application
output	O
can	O
be	O
delivered	O
in	O
a	O
variety	O
of	O
formats	O
.	O
</s>
<s>
These	O
formats	O
include	O
HTML	B-Language
,	O
plain	O
text	O
,	O
and	O
XML	B-Protocol
formatting	O
.	O
</s>
<s>
For	O
NCBI	O
's	O
web-page	O
,	O
the	O
default	O
format	O
for	O
output	O
is	O
HTML	B-Language
.	O
</s>
<s>
When	O
performing	O
a	O
BLAST	B-Application
on	O
NCBI	O
,	O
the	O
results	O
are	O
given	O
in	O
a	O
graphical	O
format	O
showing	O
the	O
hits	O
found	O
,	O
a	O
table	O
showing	O
sequence	O
identifiers	O
for	O
the	O
hits	O
with	O
scoring	O
related	O
data	O
,	O
as	O
well	O
as	O
alignments	O
for	O
the	O
sequence	O
of	O
interest	O
and	O
the	O
hits	O
received	O
with	O
corresponding	O
BLAST	B-Application
scores	O
for	O
these	O
.	O
</s>
<s>
If	O
one	O
is	O
attempting	O
to	O
search	O
for	O
a	O
proprietary	O
sequence	O
or	O
simply	O
one	O
that	O
is	O
unavailable	O
in	O
databases	O
available	O
to	O
the	O
general	O
public	O
through	O
sources	O
such	O
as	O
NCBI	O
,	O
there	O
is	O
a	O
BLAST	B-Application
program	O
available	O
for	O
download	O
to	O
any	O
computer	O
,	O
at	O
no	O
cost	O
.	O
</s>
<s>
This	O
can	O
be	O
found	O
at	O
BLAST+	O
executables	O
.	O
</s>
<s>
Databases	O
can	O
be	O
found	O
from	O
the	O
NCBI	O
site	O
,	O
as	O
well	O
as	O
from	O
Index	O
of	O
BLAST	B-Application
databases	O
(	O
FTP	O
)	O
.	O
</s>
<s>
Using	O
a	O
heuristic	B-Algorithm
method	O
,	O
BLAST	B-Application
finds	O
similar	O
sequences	O
,	O
by	O
locating	O
short	O
matches	O
between	O
the	O
two	O
sequences	O
.	O
</s>
<s>
It	O
is	O
after	O
this	O
first	O
match	O
that	O
BLAST	B-Application
begins	O
to	O
make	O
local	B-Algorithm
alignments	I-Algorithm
.	O
</s>
<s>
If	O
a	O
BLAST	B-Application
was	O
being	O
conducted	O
under	O
normal	O
conditions	O
,	O
the	O
word	O
size	O
would	O
be	O
3	O
letters	O
.	O
</s>
<s>
The	O
heuristic	B-Algorithm
algorithm	I-Algorithm
of	O
BLAST	B-Application
locates	O
all	O
common	O
three-letter	O
words	O
between	O
the	O
sequence	O
of	O
interest	O
and	O
the	O
hit	O
sequence	O
or	O
sequences	O
from	O
the	O
database	O
.	O
</s>
<s>
One	O
commonly	O
used	O
scoring	O
matrix	O
for	O
BLAST	B-Application
searches	O
is	O
BLOSUM62	O
,	O
although	O
the	O
optimal	O
scoring	O
matrix	O
depends	O
on	O
sequence	O
similarity	O
.	O
</s>
<s>
Once	O
seeding	O
has	O
been	O
conducted	O
,	O
the	O
alignment	O
which	O
is	O
only	O
3	O
residues	O
long	O
,	O
is	O
extended	O
in	O
both	O
directions	O
by	O
the	O
algorithm	O
used	O
by	O
BLAST	B-Application
.	O
</s>
<s>
If	O
this	O
score	O
is	O
higher	O
than	O
a	O
pre-determined	O
T	O
,	O
the	O
alignment	O
will	O
be	O
included	O
in	O
the	O
results	O
given	O
by	O
BLAST	B-Application
.	O
</s>
<s>
However	O
,	O
if	O
this	O
score	O
is	O
lower	O
than	O
this	O
pre-determined	O
T	O
,	O
the	O
alignment	O
will	O
cease	O
to	O
extend	O
,	O
preventing	O
the	O
areas	O
of	O
poor	O
alignment	O
from	O
being	O
included	O
in	O
the	O
BLAST	B-Application
results	O
.	O
</s>
<s>
To	O
run	O
the	O
software	O
,	O
BLAST	B-Application
requires	O
a	O
query	O
sequence	O
to	O
search	O
for	O
,	O
and	O
a	O
sequence	O
to	O
search	O
against	O
(	O
also	O
called	O
the	O
target	O
sequence	O
)	O
or	O
a	O
sequence	O
database	O
containing	O
multiple	O
such	O
sequences	O
.	O
</s>
<s>
BLAST	B-Application
will	O
find	O
sub-sequences	O
in	O
the	O
database	O
which	O
are	O
similar	O
to	O
subsequences	O
in	O
the	O
query	O
.	O
</s>
<s>
The	O
main	O
idea	O
of	O
BLAST	B-Application
is	O
that	O
there	O
are	O
often	O
High-scoring	O
Segment	O
Pairs	O
(	O
HSP	O
)	O
contained	O
in	O
a	O
statistically	O
significant	O
alignment	O
.	O
</s>
<s>
BLAST	B-Application
searches	O
for	O
high	O
scoring	O
sequence	B-Algorithm
alignments	I-Algorithm
between	O
the	O
query	O
sequence	O
and	O
the	O
existing	O
sequences	O
in	O
the	O
database	O
using	O
a	O
heuristic	B-Algorithm
approach	O
that	O
approximates	O
the	O
Smith-Waterman	B-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
However	O
,	O
the	O
exhaustive	O
Smith-Waterman	B-Algorithm
approach	O
is	O
too	O
slow	O
for	O
searching	O
large	O
genomic	O
databases	O
such	O
as	O
GenBank	O
.	O
</s>
<s>
Therefore	O
,	O
the	O
BLAST	B-Application
algorithm	O
uses	O
a	O
heuristic	B-Algorithm
approach	O
that	O
is	O
less	O
accurate	O
than	O
the	O
Smith-Waterman	B-Algorithm
algorithm	I-Algorithm
but	O
over	O
50	O
times	O
faster	O
.	O
</s>
<s>
 [ 8 ] 	O
The	O
speed	O
and	O
relatively	O
good	O
accuracy	O
of	O
BLAST	B-Application
are	O
among	O
the	O
key	O
technical	O
innovations	O
of	O
the	O
BLAST	B-Application
programs	O
.	O
</s>
<s>
An	O
overview	O
of	O
the	O
BLAST	B-Application
algorithm	O
(	O
a	O
protein	O
to	O
protein	O
search	O
)	O
is	O
as	O
follows	O
:	O
</s>
<s>
The	O
regions	O
will	O
be	O
marked	O
with	O
an	O
X	O
(	O
protein	O
sequences	O
)	O
or	O
N	O
(	O
nucleic	O
acid	O
sequences	O
)	O
and	O
then	O
be	O
ignored	O
by	O
the	O
BLAST	B-Application
program	O
.	O
</s>
<s>
This	O
step	O
is	O
one	O
of	O
the	O
main	O
differences	O
between	O
BLAST	B-Application
and	O
FASTA	B-Application
.	O
</s>
<s>
FASTA	B-Application
cares	O
about	O
all	O
of	O
the	O
common	O
words	O
in	O
the	O
database	O
and	O
query	O
sequences	O
that	O
are	O
listed	O
in	O
step	O
2	O
;	O
however	O
,	O
BLAST	B-Application
only	O
cares	O
about	O
the	O
high-scoring	O
words	O
.	O
</s>
<s>
By	O
using	O
the	O
scoring	O
matrix	O
(	O
substitution	B-Algorithm
matrix	I-Algorithm
)	O
to	O
score	O
the	O
comparison	O
of	O
each	O
residue	O
pair	O
,	O
there	O
are	O
20^3	O
possible	O
match	O
scores	O
for	O
a	O
3-letter	O
word	O
.	O
</s>
<s>
The	O
BLAST	B-Application
program	O
scans	O
the	O
database	O
sequences	O
for	O
the	O
remaining	O
high-scoring	O
word	O
,	O
such	O
as	O
PEG	O
,	O
of	O
each	O
position	O
.	O
</s>
<s>
The	O
original	O
version	O
of	O
BLAST	B-Application
stretches	O
a	O
longer	O
alignment	O
between	O
the	O
query	O
and	O
the	O
database	O
sequence	O
in	O
the	O
left	O
and	O
right	O
directions	O
,	O
from	O
the	O
position	O
where	O
the	O
exact	O
match	O
occurred	O
.	O
</s>
<s>
To	O
save	O
more	O
time	O
,	O
a	O
newer	O
version	O
of	O
BLAST	B-Application
,	O
called	O
BLAST2	O
or	O
gapped	O
BLAST	B-Application
,	O
has	O
been	O
developed	O
.	O
</s>
<s>
Finally	O
,	O
the	O
new	O
regions	O
are	O
then	O
extended	O
by	O
the	O
same	O
method	O
as	O
in	O
the	O
original	O
version	O
of	O
BLAST	B-Application
,	O
and	O
the	O
HSPs	O
 '	O
(	O
High-scoring	O
segment	O
pair	O
)	O
scores	O
of	O
the	O
extended	O
regions	O
are	O
then	O
created	O
by	O
using	O
a	O
substitution	B-Algorithm
matrix	I-Algorithm
as	O
before	O
.	O
</s>
<s>
BLAST	B-Application
next	O
assesses	O
the	O
statistical	O
significance	O
of	O
each	O
HSP	O
score	O
by	O
exploiting	O
the	O
Gumbel	O
extreme	O
value	O
distribution	O
(	O
EVD	O
)	O
.	O
</s>
<s>
(	O
It	O
is	O
proved	O
that	O
the	O
distribution	O
of	O
Smith-Waterman	B-Algorithm
local	B-Algorithm
alignment	I-Algorithm
scores	O
between	O
two	O
random	O
sequences	O
follows	O
the	O
Gumbel	O
EVD	O
.	O
</s>
<s>
For	O
local	B-Algorithm
alignments	I-Algorithm
containing	O
gaps	O
it	O
is	O
not	O
proved	O
.	O
)	O
.	O
</s>
<s>
The	O
statistical	O
parameters	O
and	O
are	O
estimated	O
by	O
fitting	O
the	O
distribution	O
of	O
the	O
un-gapped	O
local	B-Algorithm
alignment	I-Algorithm
scores	O
,	O
of	O
the	O
query	O
sequence	O
and	O
a	O
lot	O
of	O
shuffled	O
versions	O
(	O
Global	O
or	O
local	O
shuffling	O
)	O
of	O
a	O
database	O
sequence	O
,	O
to	O
the	O
Gumbel	O
extreme	O
value	O
distribution	O
.	O
</s>
<s>
Note	O
that	O
and	O
depend	O
upon	O
the	O
substitution	B-Algorithm
matrix	I-Algorithm
,	O
gap	O
penalties	O
,	O
and	O
sequence	O
composition	O
(	O
the	O
letter	O
frequencies	O
)	O
.	O
</s>
<s>
Altschul	O
and	O
Gish	O
gave	O
the	O
typical	O
values	O
,	O
,	O
,	O
and	O
,	O
for	O
un-gapped	O
local	B-Algorithm
alignment	I-Algorithm
using	O
BLOSUM62	O
as	O
the	O
substitution	B-Algorithm
matrix	I-Algorithm
.	O
</s>
<s>
This	O
expectation	O
or	O
expect	O
value	O
"	O
E	O
"	O
(	O
often	O
called	O
an	O
E	O
score	O
or	O
E-value	O
or	O
e-value	O
)	O
assessing	O
the	O
significance	O
of	O
the	O
HSP	O
score	O
for	O
un-gapped	O
local	B-Algorithm
alignment	I-Algorithm
is	O
reported	O
in	O
the	O
BLAST	B-Application
results	O
.	O
</s>
<s>
The	O
original	O
BLAST	B-Application
uses	O
the	O
Poisson	O
method	O
;	O
gapped	O
BLAST	B-Application
and	O
the	O
WU-BLAST	O
uses	O
the	O
sum-of	O
scores	O
method	O
.	O
</s>
<s>
Show	O
the	O
gapped	O
Smith-Waterman	B-Algorithm
local	B-Algorithm
alignments	I-Algorithm
of	O
the	O
query	O
and	O
each	O
of	O
the	O
matched	O
database	O
sequences	O
.	O
</s>
<s>
The	O
original	O
BLAST	B-Application
only	O
generates	O
un-gapped	O
alignments	O
including	O
the	O
initially	O
found	O
HSPs	O
individually	O
,	O
even	O
when	O
there	O
is	O
more	O
than	O
one	O
HSP	O
found	O
in	O
one	O
database	O
sequence	O
.	O
</s>
<s>
Parallel	O
BLAST	B-Application
versions	O
of	O
split	O
databases	O
are	O
implemented	O
using	O
MPI	B-Application
and	O
Pthreads	B-Operating_System
,	O
and	O
have	O
been	O
ported	O
to	O
various	O
platforms	O
including	O
Windows	B-Application
,	O
Linux	B-Application
,	O
Solaris	B-Application
,	O
Mac	B-Operating_System
OS	I-Operating_System
X	I-Operating_System
,	O
and	O
AIX	B-Application
.	O
</s>
<s>
Popular	O
approaches	O
to	O
parallelize	O
BLAST	B-Application
include	O
query	O
distribution	O
,	O
hash	O
table	O
segmentation	O
,	O
computation	O
parallelization	O
,	O
and	O
database	O
segmentation	O
(	O
partition	O
)	O
.	O
</s>
<s>
Each	O
query	O
is	O
run	O
on	O
all	O
nodes	O
in	O
parallel	O
and	O
the	O
resultant	O
BLAST	B-Application
output	O
files	O
from	O
all	O
nodes	O
merged	O
to	O
yield	O
the	O
final	O
output	O
.	O
</s>
<s>
The	O
BLAST	B-Application
program	O
can	O
either	O
be	O
downloaded	O
and	O
run	O
as	O
a	O
command-line	O
utility	O
"	O
blastall	O
"	O
or	O
accessed	O
for	O
free	O
over	O
the	O
web	O
.	O
</s>
<s>
The	O
BLAST	B-Application
web	O
server	O
,	O
hosted	O
by	O
the	O
NCBI	O
,	O
allows	O
anyone	O
with	O
a	O
web	O
browser	O
to	O
perform	O
similarity	O
searches	O
against	O
constantly	O
updated	O
databases	O
of	O
proteins	O
and	O
DNA	O
that	O
include	O
most	O
of	O
the	O
newly	O
sequenced	O
organisms	O
.	O
</s>
<s>
The	O
BLAST	B-Application
program	O
is	O
based	O
on	O
an	O
open-source	O
format	O
,	O
giving	O
everyone	O
access	O
to	O
it	O
and	O
enabling	O
them	O
to	O
have	O
the	O
ability	O
to	O
change	O
the	O
program	O
code	O
.	O
</s>
<s>
This	O
has	O
led	O
to	O
the	O
creation	O
of	O
several	O
BLAST	B-Application
"	O
spin-offs	O
"	O
.	O
</s>
<s>
There	O
are	O
now	O
a	O
handful	O
of	O
different	O
BLAST	B-Application
programs	O
available	O
,	O
which	O
can	O
be	O
used	O
depending	O
on	O
what	O
one	O
is	O
attempting	O
to	O
do	O
and	O
what	O
they	O
are	O
working	O
with	O
.	O
</s>
<s>
BLAST	B-Application
is	O
actually	O
a	O
family	O
of	O
programs	O
(	O
all	O
included	O
in	O
the	O
blastall	O
executable	O
)	O
.	O
</s>
<s>
Nucleotide-nucleotide	O
BLAST	B-Application
(	O
blastn	B-Application
)	O
This	O
program	O
,	O
given	O
a	O
DNA	O
query	O
,	O
returns	O
the	O
most	O
similar	O
DNA	O
sequences	O
from	O
the	O
DNA	O
database	O
that	O
the	O
user	O
specifies	O
.	O
</s>
<s>
Protein-protein	O
BLAST	B-Application
(	O
blastp	B-Application
)	O
This	O
program	O
,	O
given	O
a	O
protein	O
query	O
,	O
returns	O
the	O
most	O
similar	O
protein	O
sequences	O
from	O
the	O
protein	O
database	O
that	O
the	O
user	O
specifies	O
.	O
</s>
<s>
Position-Specific	O
Iterative	O
BLAST	B-Application
(	O
PSI-BLAST	O
)	O
(	O
blastpgp	O
)	O
This	O
program	O
is	O
used	O
to	O
find	O
distant	O
relatives	O
of	O
a	O
protein	O
.	O
</s>
<s>
By	O
including	O
related	O
proteins	O
in	O
the	O
search	O
,	O
PSI-BLAST	O
is	O
much	O
more	O
sensitive	O
in	O
picking	O
up	O
distant	O
evolutionary	O
relationships	O
than	O
a	O
standard	O
protein-protein	O
BLAST	B-Application
.	O
</s>
<s>
Nucleotide	O
6-frame	O
translation-nucleotide	O
6-frame	O
translation	O
(	O
tblastx	O
)	O
This	O
program	O
is	O
the	O
slowest	O
of	O
the	O
BLAST	B-Application
family	O
.	O
</s>
<s>
Large	O
numbers	O
of	O
query	O
sequences	O
(	O
megablast	O
)	O
When	O
comparing	O
large	O
numbers	O
of	O
input	O
sequences	O
via	O
the	O
command-line	O
BLAST	B-Application
,	O
"	O
megablast	O
"	O
is	O
much	O
faster	O
than	O
running	O
BLAST	B-Application
multiple	O
times	O
.	O
</s>
<s>
It	O
concatenates	O
many	O
input	O
sequences	O
together	O
to	O
form	O
a	O
large	O
sequence	O
before	O
searching	O
the	O
BLAST	B-Application
database	O
,	O
then	O
post-analyzes	O
the	O
search	O
results	O
to	O
glean	O
individual	O
alignments	O
and	O
statistical	O
values	O
.	O
</s>
<s>
Of	O
these	O
programs	O
,	O
BLASTn	B-Application
and	O
BLASTp	B-Application
are	O
the	O
most	O
commonly	O
used	O
.	O
</s>
<s>
CS-BLAST	B-Application
(	O
Context-Specific	O
BLAST	B-Application
)	O
is	O
an	O
extended	O
version	O
of	O
BLAST	B-Application
for	O
searching	O
protein	O
sequences	O
that	O
finds	O
twice	O
as	O
many	O
remotely	O
related	O
sequences	O
as	O
BLAST	B-Application
at	O
the	O
same	O
speed	O
and	O
error	O
rate	O
.	O
</s>
<s>
In	O
CS-BLAST	B-Application
,	O
the	O
mutation	O
probabilities	O
between	O
amino	O
acids	O
depend	O
not	O
only	O
on	O
the	O
single	O
amino	O
acid	O
,	O
as	O
in	O
BLAST	B-Application
,	O
but	O
also	O
on	O
its	O
local	O
sequence	O
context	O
.	O
</s>
<s>
Washington	O
University	O
produced	O
an	O
alternative	O
version	O
of	O
NCBI	O
BLAST	B-Application
,	O
called	O
WU-BLAST	O
.	O
</s>
<s>
In	O
2009	O
,	O
NCBI	O
has	O
released	O
a	O
new	O
set	O
of	O
BLAST	B-Application
executables	O
,	O
the	O
C++	B-Language
based	O
BLAST+	O
,	O
and	O
has	O
released	O
C	B-Language
versions	O
until	O
2.2.26	O
.	O
</s>
<s>
Starting	O
with	O
version	O
2.2.27	O
(	O
April	O
2013	O
)	O
,	O
only	O
BLAST+	O
executables	O
are	O
available	O
.	O
</s>
<s>
Among	O
the	O
changes	O
is	O
the	O
replacement	O
of	O
the	O
blastall	O
executable	O
with	O
separate	O
executables	O
for	O
the	O
different	O
BLAST	B-Application
programs	O
,	O
and	O
changes	O
in	O
option	O
handling	O
.	O
</s>
<s>
The	O
formatdb	B-Application
utility	O
(	O
C	B-Language
based	O
)	O
has	O
been	O
replaced	O
by	O
makeblastdb	O
(	O
C++	B-Language
based	O
)	O
and	O
databases	O
formatted	O
by	O
either	O
one	O
should	O
be	O
compatible	O
for	O
identical	O
blast	B-Application
releases	O
.	O
</s>
<s>
When	O
local	O
infrastructure	O
is	O
insufficient	O
,	O
running	O
BLAST	B-Application
on	O
a	O
cloud	O
server	O
can	O
be	O
a	O
good	O
way	O
forwards	O
as	O
it	O
makes	O
it	O
possible	O
to	O
access	O
more	O
power	O
while	O
remaining	O
with	O
standard	O
BLAST	B-Application
.	O
</s>
<s>
TimeLogic	B-Application
offers	O
an	O
FPGA-accelerated	O
implementation	O
of	O
the	O
BLAST	B-Application
algorithm	O
called	O
Tera-BLAST	O
that	O
is	O
hundreds	O
of	O
times	O
faster	O
.	O
</s>
<s>
Prior	O
to	O
their	O
acquisition	O
by	O
Qiagen	O
,	O
CLC	O
bio	O
collaborated	O
with	O
SciEngines	B-Device
GmbH	I-Device
on	O
an	O
FPGA	B-Architecture
accelerator	O
they	O
claimed	O
will	O
give	O
188x	O
acceleration	O
of	O
BLAST	B-Application
.	O
</s>
<s>
The	O
Mitrion-C	O
Open	O
Bio	O
Project	O
was	O
an	O
effort	O
to	O
port	O
BLAST	B-Application
to	O
run	O
on	O
Mitrion	B-General_Concept
FPGAs	I-General_Concept
.	O
</s>
<s>
GPU-Blast	O
is	O
an	O
accelerated	O
version	O
of	O
NCBI	O
BLASTP	B-Application
for	O
CUDA	B-Architecture
which	O
is	O
3x	O
~	O
4x	O
faster	O
than	O
NCBI	O
Blast	B-Application
.	O
</s>
<s>
CUDA-BLASTP	O
is	O
a	O
version	O
of	O
BLASTP	B-Application
that	O
is	O
GPU-accelerated	O
and	O
is	O
claimed	O
to	O
run	O
up	O
to	O
10x	O
faster	O
than	O
NCBI	O
BLAST	B-Application
.	O
</s>
<s>
G-BLASTN	O
is	O
an	O
accelerated	O
version	O
of	O
NCBI	O
blastn	B-Application
and	O
megablast	O
,	O
whose	O
speedup	O
varies	O
from	O
4x	O
to	O
14x	O
(	O
compared	O
to	O
the	O
same	O
runs	O
with	O
4	O
CPU	O
threads	O
)	O
.	O
</s>
<s>
mpiBlast	O
is	O
a	O
parallel	O
implementation	O
of	O
NCBI	O
BLAST	B-Application
using	O
Message	B-Application
Passing	I-Application
Interface	I-Application
.	O
</s>
<s>
By	O
efficiently	O
utilizing	O
distributed	O
computational	O
resources	O
through	O
database	O
fragmentation	O
,	O
query	O
segmentation	O
,	O
intelligent	O
scheduling	O
,	O
and	O
parallel	O
I/O	O
,	O
mpiBLAST	O
improves	O
NCBI	O
BLAST	B-Application
performance	O
by	O
several	O
orders	O
of	O
magnitude	O
while	O
scaling	O
to	O
hundreds	O
of	O
processors	O
.	O
</s>
<s>
Paracel	O
BLAST	B-Application
was	O
a	O
commercial	O
parallel	O
implementation	O
of	O
NCBI	O
BLAST	B-Application
,	O
supporting	O
hundreds	O
of	O
processors	O
.	O
</s>
<s>
The	O
predecessor	O
to	O
BLAST	B-Application
,	O
FASTA	B-Application
,	O
can	O
also	O
be	O
used	O
for	O
protein	O
and	O
DNA	O
similarity	O
searching	O
.	O
</s>
<s>
FASTA	B-Application
provides	O
a	O
similar	O
set	O
of	O
programs	O
for	O
comparing	O
proteins	O
to	O
protein	O
and	O
DNA	O
databases	O
,	O
DNA	O
to	O
DNA	O
and	O
protein	O
databases	O
,	O
and	O
includes	O
additional	O
programs	O
for	O
working	O
with	O
unordered	O
short	O
peptides	O
and	O
DNA	O
sequences	O
.	O
</s>
<s>
In	O
addition	O
,	O
the	O
FASTA	B-Application
package	O
provides	O
SSEARCH	O
,	O
a	O
vectorized	O
implementation	O
of	O
the	O
rigorous	O
Smith-Waterman	B-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
FASTA	B-Application
is	O
slower	O
than	O
BLAST	B-Application
,	O
but	O
provides	O
a	O
much	O
wider	O
range	O
of	O
scoring	O
matrices	O
,	O
making	O
it	O
easier	O
to	O
tailor	O
a	O
search	O
to	O
a	O
specific	O
evolutionary	O
distance	O
.	O
</s>
<s>
An	O
extremely	O
fast	O
but	O
considerably	O
less	O
sensitive	O
alternative	O
to	O
BLAST	B-Application
is	O
BLAT	B-Application
(	O
Blast	B-Application
Like	O
Alignment	O
Tool	O
)	O
.	O
</s>
<s>
While	O
BLAST	B-Application
does	O
a	O
linear	O
search	O
,	O
BLAT	B-Application
relies	O
on	O
k-mer	O
indexing	O
the	O
database	O
,	O
and	O
can	O
thus	O
often	O
find	O
seeds	O
faster	O
.	O
</s>
<s>
Another	O
software	O
alternative	O
similar	O
to	O
BLAT	B-Application
is	O
PatternHunter	B-Application
.	O
</s>
<s>
New	O
alignment	B-Application
programs	I-Application
tailored	O
for	O
this	O
use	O
typically	O
use	O
BWT-indexing	O
of	O
the	O
target	O
database	O
(	O
typically	O
a	O
genome	O
)	O
.	O
</s>
<s>
Example	O
alignment	B-Application
programs	I-Application
are	O
BWA	O
,	O
SOAP	B-Application
,	O
and	O
Bowtie	O
.	O
</s>
<s>
For	O
protein	O
identification	O
,	O
searching	O
for	O
known	O
domains	O
(	O
for	O
instance	O
from	O
Pfam	O
)	O
by	O
matching	O
with	O
Hidden	O
Markov	O
Models	O
is	O
a	O
popular	O
alternative	O
,	O
such	O
as	O
HMMER	B-Language
.	O
</s>
<s>
An	O
alternative	O
to	O
BLAST	B-Application
for	O
comparing	O
two	O
banks	O
of	O
sequences	O
is	O
PLAST	O
.	O
</s>
<s>
PLAST	O
provides	O
a	O
high-performance	O
general	O
purpose	O
bank	O
to	O
bank	O
sequence	B-Algorithm
similarity	I-Algorithm
search	I-Algorithm
tool	O
relying	O
on	O
the	O
PLAST	O
and	O
ORIS	O
algorithms	O
.	O
</s>
<s>
Results	O
of	O
PLAST	O
are	O
very	O
similar	O
to	O
BLAST	B-Application
,	O
but	O
PLAST	O
is	O
significantly	O
faster	O
and	O
capable	O
of	O
comparing	O
large	O
sets	O
of	O
sequences	O
with	O
a	O
small	O
memory	O
(	O
i.e.	O
</s>
<s>
The	O
open-source	O
software	O
MMseqs	O
is	O
an	O
alternative	O
to	O
BLAST/PSI	O
-BLAST	O
,	O
which	O
improves	O
on	O
current	O
search	O
tools	O
over	O
the	O
full	O
range	O
of	O
speed-sensitivity	O
trade-off	O
,	O
achieving	O
sensitivities	O
better	O
than	O
PSI-BLAST	O
at	O
more	O
than	O
400	O
times	O
its	O
speed	O
.	O
</s>
<s>
OptCAM	O
is	O
an	O
example	O
of	O
such	O
approaches	O
and	O
is	O
shown	O
to	O
be	O
faster	O
than	O
BLAST	B-Application
.	O
</s>
<s>
While	O
both	O
Smith-Waterman	B-Algorithm
and	O
BLAST	B-Application
are	O
used	O
to	O
find	O
homologous	O
sequences	O
by	O
searching	O
and	O
comparing	O
a	O
query	O
sequence	O
with	O
those	O
in	O
the	O
databases	O
,	O
they	O
do	O
have	O
their	O
differences	O
.	O
</s>
<s>
Due	O
to	O
the	O
fact	O
that	O
BLAST	B-Application
is	O
based	O
on	O
a	O
heuristic	B-Algorithm
algorithm	I-Algorithm
,	O
the	O
results	O
received	O
through	O
BLAST	B-Application
,	O
in	O
terms	O
of	O
the	O
hits	O
found	O
,	O
may	O
not	O
be	O
the	O
best	O
possible	O
results	O
,	O
as	O
it	O
will	O
not	O
provide	O
you	O
with	O
all	O
the	O
hits	O
within	O
the	O
database	O
.	O
</s>
<s>
BLAST	B-Application
misses	O
hard	O
to	O
find	O
matches	O
.	O
</s>
<s>
A	O
better	O
alternative	O
in	O
order	O
to	O
find	O
the	O
best	O
possible	O
results	O
would	O
be	O
to	O
use	O
the	O
Smith-Waterman	B-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
This	O
method	O
varies	O
from	O
the	O
BLAST	B-Application
method	O
in	O
two	O
areas	O
,	O
accuracy	O
and	O
speed	O
.	O
</s>
<s>
The	O
Smith-Waterman	B-Algorithm
option	O
provides	O
better	O
accuracy	O
,	O
in	O
that	O
it	O
finds	O
matches	O
that	O
BLAST	B-Application
cannot	O
,	O
because	O
it	O
does	O
not	O
miss	O
any	O
information	O
.	O
</s>
<s>
However	O
,	O
when	O
compared	O
to	O
BLAST	B-Application
,	O
it	O
is	O
more	O
time	O
consuming	O
,	O
not	O
to	O
mention	O
that	O
it	O
requires	O
large	O
amounts	O
of	O
computer	O
usage	O
and	O
space	O
.	O
</s>
<s>
However	O
,	O
technologies	O
to	O
speed	O
up	O
the	O
Smith-Waterman	B-Algorithm
process	O
have	O
been	O
found	O
to	O
improve	O
the	O
time	O
necessary	O
to	O
perform	O
a	O
search	O
dramatically	O
.	O
</s>
<s>
These	O
technologies	O
include	O
FPGA	B-Architecture
chips	O
and	O
SIMD	B-Device
technology	O
.	O
</s>
<s>
In	O
order	O
to	O
receive	O
better	O
results	O
from	O
BLAST	B-Application
,	O
the	O
settings	O
can	O
be	O
changed	O
from	O
their	O
default	O
settings	O
.	O
</s>
<s>
The	O
settings	O
available	O
for	O
change	O
are	O
E-Value	O
,	O
gap	O
costs	O
,	O
filters	O
,	O
word	O
size	O
,	O
and	O
substitution	B-Algorithm
matrix	I-Algorithm
.	O
</s>
<s>
Note	O
,	O
that	O
the	O
algorithm	O
used	O
for	O
BLAST	B-Application
was	O
developed	O
from	O
the	O
algorithm	O
used	O
for	O
Smith-Waterman	B-Algorithm
.	O
</s>
<s>
BLAST	B-Application
employs	O
an	O
alignment	O
which	O
finds	O
"	O
local	B-Algorithm
alignments	I-Algorithm
between	O
sequences	O
by	O
finding	O
short	O
matches	O
and	O
from	O
these	O
initial	O
matches	O
(	O
local	O
)	O
alignments	O
are	O
created	O
"	O
.	O
</s>
<s>
To	O
help	O
users	O
interpreting	O
BLAST	B-Application
results	O
,	O
different	O
software	O
is	O
available	O
.	O
</s>
<s>
integrated	O
BLAST	B-Application
environments	O
:	O
PLAN	O
,	O
BlastStation-Free	O
,	O
</s>
<s>
BLAST	B-Application
output	O
parsers	O
:	O
MuSeqBox	O
,	O
Zerg	O
,	O
BioParser	O
,	O
BLAST-Explorer	O
,	O
</s>
<s>
specialized	O
BLAST-related	O
tools	O
:	O
,	O
BLAST2GENE	O
,	O
BOV	O
,	O
</s>
<s>
Example	O
visualisations	O
of	O
BLAST	B-Application
results	O
are	O
shown	O
in	O
Figure	O
4	O
and	O
5	O
.	O
</s>
<s>
BLAST	B-Application
can	O
be	O
used	O
for	O
several	O
purposes	O
.	O
</s>
<s>
Identifying	O
species	O
With	O
the	O
use	O
of	O
BLAST	B-Application
,	O
you	O
can	O
possibly	O
correctly	O
identify	O
a	O
species	O
or	O
find	O
homologous	O
species	O
.	O
</s>
<s>
Locating	O
domains	O
When	O
working	O
with	O
a	O
protein	O
sequence	O
you	O
can	O
input	O
it	O
into	O
BLAST	B-Application
,	O
to	O
locate	O
known	O
domains	O
within	O
the	O
sequence	O
of	O
interest	O
.	O
</s>
<s>
Establishing	O
phylogeny	O
Using	O
the	O
results	O
received	O
through	O
BLAST	B-Application
you	O
can	O
create	O
a	O
phylogenetic	O
tree	O
using	O
the	O
BLAST	B-Application
web-page	O
.	O
</s>
<s>
Phylogenies	O
based	O
on	O
BLAST	B-Application
alone	O
are	O
less	O
reliable	O
than	O
other	O
purpose-built	O
computational	O
phylogenetic	O
methods	O
,	O
so	O
should	O
only	O
be	O
relied	O
upon	O
for	O
"	O
first	O
pass	O
"	O
phylogenetic	O
analyses	O
.	O
</s>
<s>
DNA	O
mapping	O
When	O
working	O
with	O
a	O
known	O
species	O
,	O
and	O
looking	O
to	O
sequence	O
a	O
gene	O
at	O
an	O
unknown	O
location	O
,	O
BLAST	B-Application
can	O
compare	O
the	O
chromosomal	O
position	O
of	O
the	O
sequence	O
of	O
interest	O
,	O
to	O
relevant	O
sequences	O
in	O
the	O
database(s )	O
.	O
</s>
<s>
NCBI	O
has	O
a	O
"	O
Magic-BLAST	O
"	O
tool	O
built	O
around	O
BLAST	B-Application
for	O
this	O
purpose	O
.	O
</s>
<s>
Comparison	O
When	O
working	O
with	O
genes	O
,	O
BLAST	B-Application
can	O
locate	O
common	O
genes	O
in	O
two	O
related	O
species	O
,	O
and	O
can	O
be	O
used	O
to	O
map	O
annotations	O
from	O
one	O
organism	O
to	O
another	O
.	O
</s>
