<s>
The	O
Viral	B-Application
Bioinformatics	I-Application
Resource	I-Application
Center	I-Application
(	O
VBRC	B-Application
)	O
is	O
an	O
online	O
resource	O
providing	O
access	O
to	O
a	O
database	O
of	O
curated	O
viral	O
genomes	O
and	O
a	O
variety	O
of	O
tools	O
for	O
bioinformatic	O
genome	O
analysis	O
.	O
</s>
<s>
The	O
VBRC	B-Application
is	O
now	O
supported	O
by	O
Dr.	O
Chris	O
Upton	O
at	O
the	O
University	O
of	O
Victoria	O
.	O
</s>
<s>
The	O
curated	O
VBRC	B-Application
database	O
contains	O
all	O
publicly	O
available	O
genomic	O
sequences	O
for	O
poxviruses	O
and	O
African	O
Swine	O
Fever	O
Viruses	O
(	O
ASFV	O
)	O
.	O
</s>
<s>
protein	O
families	O
)	O
based	O
on	O
pre-run	O
BLASTP	B-Application
sequence	B-Algorithm
similarity	I-Algorithm
searches	I-Algorithm
.	O
</s>
<s>
The	O
curated	O
database	O
is	O
accessed	O
through	O
VOCS	O
(	O
Viral	O
Orthologous	O
Clusters	O
)	O
,	O
a	O
downloadable	O
Java-based	O
user	O
interface	O
,	O
and	O
acts	O
as	O
the	O
central	O
information	O
source	O
for	O
other	O
programs	O
of	O
the	O
VBRC	B-Application
workbench	O
.	O
</s>
<s>
These	O
programs	O
serve	O
a	O
variety	O
of	O
bioinformatic	O
analysis	O
functions	O
(	O
whole	O
-	O
or	O
subgenome	O
alignments	B-Algorithm
,	O
genome	O
display	O
,	O
and	O
several	O
types	O
of	O
gene/protein	O
sequence	O
analysis	O
)	O
.	O
</s>
<s>
The	O
VBRC	B-Application
covers	O
the	O
following	O
viruses	O
:	O
</s>
<s>
The	O
VBRC	B-Application
database	O
stores	O
viral	O
bioinformatic	O
data	O
on	O
three	O
levels	O
:	O
</s>
<s>
This	O
level	O
is	O
a	O
distinguishing	O
feature	O
of	O
the	O
VBRC	B-Application
database	O
.	O
</s>
<s>
Each	O
annotated	O
gene	O
,	O
after	O
it	O
has	O
been	O
entered	O
into	O
the	O
database	O
,	O
is	O
subjected	O
to	O
BLASTP	B-Application
searching	O
against	O
all	O
other	O
genes	O
already	O
in	O
the	O
database	O
.	O
</s>
<s>
VBRC	B-Application
provides	O
researchers	O
with	O
a	O
wide	O
variety	O
of	O
database-linked	O
tools	O
.	O
</s>
<s>
Additional	O
analysis	O
tools	O
such	O
as	O
BLAST	B-Application
searches	O
,	O
genome	O
maps	O
,	O
genome	O
or	O
gene	O
alignment	O
,	O
phylogenetic	O
trees	O
,	O
etc	O
.	O
</s>
<s>
VGO	O
(	O
Viral	O
Genome	O
Organizer	O
)	O
VGO	O
is	O
a	O
Java-based	O
interface	O
used	O
for	O
viewing	O
and	O
searching	O
viral	O
genome	O
sequences	O
.	O
</s>
<s>
Together	O
with	O
a	O
graphical	O
representation	O
of	O
the	O
selected	O
VBRC	B-Application
(	O
or	O
user-supplied	O
)	O
genome	O
,	O
the	O
program	O
displays	O
information	O
relevant	O
to	O
a	O
genome	O
of	O
interest	O
,	O
including	O
its	O
genes	O
,	O
ORFs	O
and	O
start/stop	O
codons	O
.	O
</s>
<s>
Tools	O
are	O
provided	O
allowing	O
the	O
user	O
to	O
perform	O
regular	B-Language
expression	I-Language
,	O
a	O
fuzzy	O
motif	O
,	O
and	O
masslist	O
searches	O
.	O
</s>
<s>
BBB	O
(	O
Base-by-Base	O
)	O
Base-By-Base	O
is	O
a	O
platform-independent	O
(	O
Java-based	O
)	O
,	O
whole-genome	O
pairwise	O
and	O
multiple	O
alignment	O
editor	O
.	O
</s>
<s>
Annotations	O
from	O
the	O
VBRC	B-Application
database	O
or	O
user-supplied	O
files	O
are	O
displayed	O
alongside	O
each	O
sequence	O
.	O
</s>
<s>
Although	O
Base-By-Base	O
was	O
intended	O
as	O
an	O
editor	O
and	O
viewer	O
for	O
alignments	B-Algorithm
of	O
highly	O
similar	O
sequences	O
,	O
it	O
also	O
generates	O
multiple	O
alignments	B-Algorithm
using	O
Clustal	O
Omega	O
,	O
T-Coffee	O
and	O
MUSCLE	O
.	O
</s>
<s>
Edit	O
functions	O
are	O
provided	O
to	O
allow	O
users	O
to	O
fine-tune	O
such	O
alignments	B-Algorithm
manually	O
;	O
users	O
may	O
also	O
annotate	O
genomes	O
with	O
comments	O
or	O
primer	O
sequences	O
.	O
</s>
<s>
JDotter	O
JDotter	O
is	O
a	O
Java-based	O
user	O
interface	O
providing	O
VBRC-linked	O
access	O
to	O
the	O
Linux	O
version	O
of	O
Dotter	O
.	O
</s>
<s>
JDotter	O
can	O
both	O
access	O
pre-processed	O
dotplots	B-Application
of	O
the	O
genome	O
and	O
gene	O
(	O
DNA	O
or	O
protein	O
)	O
sequences	O
available	O
in	O
the	O
VBRC	B-Application
database	O
,	O
and	O
take	O
user	O
input	O
for	O
generation	O
of	O
new	O
dotplots	B-Application
.	O
</s>
<s>
VBRC	B-Application
provides	O
a	O
number	O
of	O
additional	O
Java-based	O
analysis	O
tools	O
on	O
its	O
website	O
.	O
</s>
<s>
regular	B-Language
expression	I-Language
searches	O
,	O
DNA	O
skew	O
plotting	O
)	O
and	O
,	O
though	O
they	O
can	O
be	O
accessed	O
as	O
stand-alone	O
programs	O
with	O
user-supplied	O
input	O
,	O
most	O
have	O
increased	O
utility	O
when	O
launched	O
from	O
the	O
central	O
VOCS	O
application	O
with	O
VBRC-supplied	O
data	O
.	O
</s>
<s>
Sequence	O
Searcher	O
performs	O
regular	B-Language
expression	I-Language
and	O
fuzzy	O
motif	O
searches	O
of	O
DNA	O
or	O
protein	O
sequences	O
,	O
and	O
is	O
built	O
into	O
VOCS	O
.	O
</s>
<s>
NAP	O
(	O
Nucleotide	O
Amino	O
Acid	O
Alignment	O
)	O
is	O
a	O
Java	B-Language
interface	O
to	O
napC	O
,	O
a	O
program	O
designed	O
to	O
align	O
a	O
nucleotide	O
and	O
protein	O
sequence	O
,	O
taking	O
terminal	O
gaps	O
and	O
insertion/deletion	O
mutations	O
into	O
account	O
.	O
</s>
<s>
GraphDNA	O
provides	O
DNA	O
skews	O
and	O
walks	O
(	O
a	O
Cartesian	O
plane-based	O
representation	O
of	O
nucleotide	O
content	O
)	O
from	O
a	O
VBRC	B-Application
database	O
-	O
or	O
user-supplied	O
DNA	O
sequence	O
.	O
</s>
<s>
Hydrophobicity	O
Plotter	O
generates	O
a	O
hydrophobicity	O
graph	O
for	O
a	O
VBRC	B-Application
database	O
-	O
or	O
user-supplied	O
protein	O
sequence	O
.	O
</s>
