<s>
TimeLogic	B-Application
is	O
the	O
bioinformatics	O
division	O
of	O
Active	O
Motif	O
,	O
Inc	O
.	O
</s>
<s>
TimeLogic	B-Application
develops	O
FPGA-accelerated	O
tools	O
for	O
biological	O
sequence	B-Algorithm
comparison	I-Algorithm
in	O
the	O
field	O
of	O
high	O
performance	O
bioinformatics	O
and	O
biocomputing	O
.	O
</s>
<s>
TimeLogic	B-Application
was	O
founded	O
in	O
1981	O
by	O
James	O
W	O
.	O
(	O
Jim	O
)	O
Lindelien	O
and	O
developed	O
one	O
of	O
the	O
first	O
commercial	O
hardware-accelerated	B-General_Concept
tools	O
for	O
bioinformatics	O
,	O
an	O
FPGA-accelerated	O
version	O
of	O
the	O
Smith-Waterman	B-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
TimeLogic	B-Application
's	O
DeCypher	O
systems	O
have	O
expanded	O
to	O
provide	O
accelerated	O
implementations	O
of	O
the	O
ubiquitous	O
bioinformatics	O
algorithms	O
BLAST	B-Application
,	O
Smith-Waterman	B-Algorithm
,	O
and	O
HMMER	B-Language
using	O
field	B-Architecture
programmable	I-Architecture
gate	I-Architecture
array	I-Architecture
(	O
FPGA	B-Architecture
)	O
technology	O
.	O
</s>
<s>
In	O
2003	O
,	O
TimeLogic	B-Application
was	O
acquired	O
by	O
Active	O
Motif	O
,	O
a	O
biotechnology	O
reagent	O
company	O
started	O
by	O
Invitrogen	O
co-founder	O
Joseph	O
Fernandez	O
.	O
</s>
<s>
In	O
2008	O
,	O
TimeLogic	B-Application
formed	O
a	O
partnership	O
with	O
Biomatters	O
to	O
integrate	O
Geneious	O
Pro	O
with	O
the	O
accelerated	O
algorithms	O
on	O
DeCypher	O
systems	O
.	O
</s>
<s>
In	O
2011	O
,	O
TimeLogic	B-Application
formed	O
a	O
partnership	O
with	O
Bielefeld	O
University	O
's	O
Center	O
for	O
Biotechnology	O
(	O
CeBiTec	O
)	O
to	O
jointly	O
develop	O
accelerated	O
computational	O
tools	O
.	O
</s>
<s>
In	O
1997	O
,	O
the	O
annotation	O
of	O
the	O
first	O
complete	O
sequence	O
of	O
the	O
E	O
.	O
coli	O
K12	O
genome	O
used	O
DeCypher	O
Smith-Waterman	B-Algorithm
to	O
determine	O
the	O
function	O
of	O
new	O
translated	O
sequences	O
.	O
</s>
<s>
In	O
2004	O
,	O
a	O
high	O
throughput	O
genomic	O
approach	O
to	O
the	O
study	O
of	O
horizontal	O
gene	O
transfer	O
in	O
plant-parasitic	O
nematodes	O
was	O
conducted	O
using	O
DeCypher	O
Tera-BLAST	O
,	O
Timelogic	B-Application
's	O
implementation	O
of	O
the	O
BLAST	B-Application
algorithm	O
.	O
</s>
<s>
Dr.	O
Craig	O
Venter	O
credited	O
TimeLogic	B-Application
in	O
his	O
biography	O
,	O
noting	O
that	O
the	O
DeCypher	O
system	O
performed	O
"	O
an	O
order	O
of	O
magnitude	O
or	O
two	O
more	O
than	O
had	O
been	O
achieved	O
before	O
.	O
</s>
<s>
In	O
2011	O
,	O
a	O
global	O
assessment	O
of	O
the	O
genomic	O
variation	O
in	O
cattle	O
was	O
conducted	O
using	O
DeCypher	O
Tera-BLAST	O
"	O
to	O
accurately	O
detect	O
chromosomal	O
positions	O
of	O
the	O
SNP	O
sites.	O
"	O
</s>
<s>
DeCypher	O
Server	O
is	O
a	O
high	O
performance	O
server	O
with	O
the	O
DeCypher	O
Similarity	O
Search	O
Engine	O
FPGA-based	O
accelerator	O
that	O
can	O
be	O
reprogrammed	O
on	O
the	O
fly	O
to	O
run	O
all	O
of	O
TimeLogic	B-Application
's	O
accelerated	O
search	O
algorithms	O
.	O
</s>
<s>
Tera-BLAST	O
is	O
an	O
accelerated	O
BLAST	B-Application
algorithm	O
implementation	O
,	O
which	O
includes	O
Tera-BLASTN	O
,	O
Tera-BLASTP	O
,	O
Tera-BLASTX	O
,	O
Tera-TBLASTN	O
,	O
and	O
Tera-TBLASTX	O
.	O
</s>
<s>
Tera-BLAST	O
also	O
includes	O
Tera-Probe	O
,	O
a	O
proprietary	O
algorithm	O
for	O
probe	O
design	O
.	O
</s>
<s>
DeCypher	O
Smith-Waterman	B-Algorithm
is	O
an	O
accelerated	O
Smith-Waterman	B-Algorithm
algorithm	I-Algorithm
implementation	O
,	O
which	O
also	O
includes	O
FrameSearch	O
.	O
</s>
<s>
DeCypherHMM	O
is	O
an	O
accelerated	O
HMMER	B-Language
algorithm	O
implementation	O
,	O
which	O
also	O
includes	O
HFST	O
,	O
a	O
frameshift	O
tolerant	O
HMM	O
search	O
.	O
</s>
