<s>
PatternHunter	B-Application
is	O
a	O
commercially	O
available	O
homology	O
search	O
instrument	O
software	O
that	O
uses	O
sequence	B-Algorithm
alignment	I-Algorithm
techniques	O
.	O
</s>
<s>
Several	O
sequence	B-Algorithm
alignment	I-Algorithm
programs	O
have	O
been	O
developed	O
to	O
determine	O
homology	O
between	O
genes	O
.	O
</s>
<s>
These	O
include	O
FASTA	B-Application
,	O
the	O
BLAST	B-Application
family	O
,	O
QUASAR	O
,	O
MUMmer	B-Application
,	O
SENSEI	O
,	O
SIM	O
,	O
and	O
REPuter	O
.	O
</s>
<s>
They	O
mostly	O
use	O
Smith-Waterman	B-Algorithm
alignment	O
technique	O
,	O
which	O
compares	O
bases	O
against	O
other	O
bases	O
,	O
but	O
is	O
too	O
slow	O
.	O
</s>
<s>
BLAST	B-Application
makes	O
an	O
improvement	O
to	O
this	O
technique	O
by	O
establishing	O
brief	O
,	O
precise	O
seed	O
matches	O
that	O
it	O
later	O
joins	O
up	O
to	O
form	O
longer	O
alignments	O
.	O
</s>
<s>
Techniques	O
such	O
as	O
MUMmer	B-Application
and	O
QUASAR	O
employ	O
suffix	O
trees	O
,	O
which	O
are	O
supposed	O
to	O
handle	O
exact	O
matches	O
.	O
</s>
<s>
PatternHunter	B-Application
utilizes	O
numerous	O
seeds	O
(	O
tiny	O
search	O
strings	O
)	O
with	O
optimal	O
intervals	O
between	O
them	O
.	O
</s>
<s>
PatternHunter	B-Application
strikes	O
a	O
delicate	O
balance	O
in	O
this	O
area	O
by	O
providing	O
optimal	O
spacing	O
between	O
search	O
strings	O
.	O
</s>
<s>
It	O
uses	O
alternate	O
k	O
(	O
k	O
=	O
11	O
)	O
letters	O
as	O
seeds	O
in	O
contrast	O
with	O
BLAST	B-Application
,	O
which	O
utilizes	O
successive	O
k	O
letters	O
as	O
seeds	O
.	O
</s>
<s>
The	O
first	O
stage	O
in	O
PatternHunter	B-Application
analysis	O
entails	O
a	O
filtering	O
phase	O
where	O
the	O
program	O
hunts	O
for	O
matches	O
in	O
k	O
alternating	O
points	O
as	O
denoted	O
by	O
the	O
most	O
advantageous	O
pattern	O
.	O
</s>
<s>
The	O
second	O
stage	O
is	O
the	O
alignment	O
phase	O
,	O
which	O
is	O
identical	O
to	O
BLAST	B-Application
.	O
</s>
<s>
In	O
addition	O
,	O
it	O
is	O
possible	O
to	O
use	O
more	O
than	O
one	O
seed	O
at	O
a	O
go	O
with	O
PatternHunter	B-Application
.	O
</s>
<s>
PatternHunter	B-Application
takes	O
a	O
short	O
time	O
to	O
analyze	O
all	O
types	O
of	O
sequences	O
.	O
</s>
<s>
When	O
compared	O
to	O
other	O
tools	O
,	O
PatternHunter	B-Application
exhibits	O
speeds	O
that	O
are	O
approximately	O
a	O
hundred	O
times	O
faster	O
than	O
BLAST	B-Application
and	O
Mega	O
BLAST	B-Application
.	O
</s>
<s>
These	O
speeds	O
are	O
3000-fold	O
those	O
attained	O
from	O
a	O
Smith-Waterman	B-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
In	O
terms	O
of	O
sensitivity	O
,	O
it	O
is	O
possible	O
to	O
attain	O
the	O
optimum	O
sensitivity	O
with	O
PatternHunter	B-Application
while	O
still	O
retaining	O
the	O
same	O
speed	O
as	O
a	O
conventional	O
BLAST	B-Application
search	O
.	O
</s>
<s>
The	O
designing	O
of	O
PatternHunter	B-Application
uses	O
Java	B-Device
technology	I-Device
.	O
</s>
<s>
Consequently	O
,	O
the	O
program	O
runs	O
smoothly	O
when	O
installed	O
in	O
any	O
Java	B-Device
1.4	O
environments	O
.	O
</s>
<s>
PatternHunter	B-Application
has	O
been	O
improved	O
to	O
an	O
upgraded	O
PatternHunter	B-Application
II	O
version	O
,	O
which	O
hastens	O
DNA-protein	O
searches	O
a	O
hundredfold	O
without	O
altering	O
the	O
sensitivity	O
.	O
</s>
<s>
However	O
,	O
there	O
are	O
plans	O
to	O
improve	O
PatternHunter	B-Application
to	O
attain	O
the	O
high	O
sensitivity	O
of	O
the	O
Smith	O
-	O
Waterman	O
tool	O
while	O
obtaining	O
BLAST	B-Application
pace	O
.	O
</s>
<s>
A	O
novel	O
translated	O
PatternHunter	B-Application
that	O
intends	O
to	O
hasten	O
tBLASTx	O
.	O
</s>
