<s>
BioJava	B-Language
is	O
an	O
open-source	B-Application
software	I-Application
project	O
dedicated	O
to	O
provide	O
Java	B-Language
tools	O
to	O
process	O
biological	O
data	O
.	O
</s>
<s>
BioJava	B-Language
is	O
a	O
set	O
of	O
library	B-Library
functions	I-Library
written	O
in	O
the	O
programming	O
language	O
Java	B-Language
for	O
manipulating	O
sequences	O
,	O
protein	O
structures	O
,	O
file	O
parsers	O
,	O
Common	B-Architecture
Object	I-Architecture
Request	I-Architecture
Broker	I-Architecture
Architecture	I-Architecture
(	O
CORBA	B-Architecture
)	O
interoperability	O
,	O
Distributed	O
Annotation	O
System	O
(	O
DAS	O
)	O
,	O
access	O
to	O
AceDB	O
,	O
dynamic	O
programming	O
,	O
and	O
simple	O
statistical	O
routines	O
.	O
</s>
<s>
BioJava	B-Language
supports	O
a	O
huge	O
range	O
of	O
data	O
,	O
starting	O
from	O
DNA	O
and	O
protein	O
sequences	O
to	O
the	O
level	O
of	O
3D	O
protein	O
structures	O
.	O
</s>
<s>
The	O
BioJava	B-Language
libraries	O
are	O
useful	O
for	O
automating	O
many	O
daily	O
and	O
mundane	O
bioinformatics	O
tasks	O
such	O
as	O
to	O
parsing	O
a	O
Protein	O
Data	O
Bank	O
(	O
PDB	O
)	O
file	O
,	O
interacting	O
with	O
Jmol	O
and	O
many	O
more	O
.	O
</s>
<s>
This	O
application	B-Application
programming	I-Application
interface	I-Application
(	O
API	B-Application
)	O
provides	O
various	O
file	O
parsers	O
,	O
data	O
models	O
and	O
algorithms	O
to	O
facilitate	O
working	O
with	O
the	O
standard	O
data	O
formats	O
and	O
enables	O
rapid	O
application	O
development	O
and	O
analysis	O
.	O
</s>
<s>
Additional	O
projects	O
from	O
BioJava	B-Language
include	O
rcsb-sequenceviewer	O
,	O
biojava-http	O
,	O
biojava-spark	O
,	O
and	O
rcsb-viewers	O
.	O
</s>
<s>
BioJava	B-Language
provides	O
software	O
modules	O
for	O
many	O
of	O
the	O
typical	O
tasks	O
of	O
bioinformatics	O
programming	O
.	O
</s>
<s>
The	O
BioJava	B-Language
project	O
grew	O
out	O
of	O
work	O
by	O
Thomas	O
Down	O
and	O
Matthew	O
Pocock	O
to	O
create	O
an	O
API	B-Application
to	O
simplify	O
development	O
of	O
Java-based	O
Bioinformatics	O
tools	O
.	O
</s>
<s>
BioJava	B-Language
is	O
an	O
active	O
open	O
source	O
project	O
that	O
has	O
been	O
developed	O
over	O
more	O
than	O
12	O
years	O
and	O
by	O
more	O
than	O
60	O
developers	O
.	O
</s>
<s>
BioJava	B-Language
is	O
one	O
of	O
a	O
number	O
of	O
Bio*	O
projects	O
designed	O
to	O
reduce	O
code	O
duplication	O
.	O
</s>
<s>
Examples	O
of	O
such	O
projects	O
that	O
fall	O
under	O
Bio*	O
apart	O
from	O
BioJava	B-Language
are	O
BioPython	B-Library
,	O
BioPerl	B-Application
,	O
BioRuby	B-Application
,	O
EMBOSS	O
etc	O
.	O
</s>
<s>
In	O
October	O
2012	O
,	O
the	O
first	O
paper	O
on	O
BioJava	B-Language
was	O
published	O
.	O
</s>
<s>
This	O
paper	O
detailed	O
BioJava	B-Language
's	O
modules	O
,	O
functionalities	O
,	O
and	O
purpose	O
.	O
</s>
<s>
The	O
most	O
recent	O
paper	O
on	O
BioJava	B-Language
was	O
written	O
in	O
February	O
2017	O
.	O
</s>
<s>
This	O
paper	O
detailed	O
a	O
new	O
tool	O
named	O
BioJava-ModFinder	O
.	O
</s>
<s>
More	O
than	O
30,000	O
structures	O
with	O
protein	O
modifications	O
were	O
identified	O
by	O
using	O
BioJava-ModFinder	O
and	O
can	O
be	O
found	O
on	O
the	O
RCSB	O
PDB	O
website	O
.	O
</s>
<s>
In	O
the	O
year	O
2008	O
,	O
BioJava	B-Language
's	O
first	O
Application	O
note	O
was	O
published	O
.	O
</s>
<s>
It	O
was	O
migrated	O
from	O
its	O
original	O
CVS	O
repository	O
to	O
GitHub	B-Application
in	O
April	O
2013	O
.	O
</s>
<s>
The	O
project	O
has	O
been	O
moved	O
to	O
a	O
separate	O
repository	O
,	O
BioJava-legacy	O
,	O
and	O
is	O
still	O
maintained	O
for	O
minor	O
changes	O
and	O
bug	O
fixes	O
.	O
</s>
<s>
The	O
aim	O
of	O
this	O
release	O
was	O
to	O
rewrite	O
BioJava	B-Language
so	O
that	O
it	O
could	O
be	O
modularized	O
into	O
small	O
,	O
reusable	O
components	O
.	O
</s>
<s>
The	O
new	O
approach	O
seen	O
in	O
BioJava	B-Language
3	O
was	O
modeled	O
after	O
the	O
Apache	B-Language
Commons	I-Language
.	O
</s>
<s>
This	O
version	O
brought	O
many	O
new	O
features	O
and	O
improvements	O
to	O
the	O
packages	O
biojava-core	O
,	O
biojava-structure	O
,	O
biojava-structure-gui	O
,	O
biojava-phylo	O
,	O
as	O
well	O
as	O
others	O
.	O
</s>
<s>
BioJava	B-Language
4.2.0	O
was	O
the	O
first	O
release	O
to	O
be	O
available	O
using	O
Maven	B-Language
from	O
the	O
Maven	B-Language
Central	O
.	O
</s>
<s>
BioJava	B-Language
5.0.0	O
is	O
the	O
first	O
released	O
based	O
on	O
Java	B-Language
8	O
which	O
introduces	O
the	O
use	O
of	O
lambda	B-General_Concept
functions	I-General_Concept
and	O
streaming	O
API	B-Application
calls	O
.	O
</s>
<s>
There	O
were	O
also	O
major	O
changes	O
to	O
biojava-structure	O
module	O
.	O
</s>
<s>
Some	O
of	O
the	O
other	O
improvements	O
include	O
optimizations	O
in	O
the	O
biojava-structure	O
module	O
to	O
improve	O
symmetry	O
detection	O
and	O
added	O
support	O
for	O
MMTF	O
formats	O
.	O
</s>
<s>
BioJava	B-Language
3	O
is	O
a	O
clear	O
departure	O
from	O
the	O
version	O
1	O
series	O
.	O
</s>
<s>
It	O
now	O
consists	O
of	O
several	O
independent	O
modules	O
built	O
using	O
an	O
automation	O
tool	O
called	O
Apache	B-Language
Maven	I-Language
.	O
</s>
<s>
These	O
modules	O
provide	O
state-of-the-art	O
tools	O
for	O
protein	O
structure	O
comparison	O
,	O
pairwise	O
and	O
multiple	O
sequence	B-Algorithm
alignments	I-Algorithm
,	O
working	O
with	O
DNA	O
and	O
protein	O
sequences	O
,	O
analysis	O
of	O
amino	O
acid	O
properties	O
,	O
detecting	O
protein	O
modifications	O
,	O
predicting	O
disordered	O
regions	O
in	O
proteins	O
,	O
and	O
parsers	O
for	O
common	O
file	O
formats	O
using	O
a	O
biologically	O
meaningful	O
data	O
model	O
.	O
</s>
<s>
The	O
original	O
code	O
has	O
been	O
moved	O
into	O
a	O
separate	O
BioJava	B-Language
legacy	O
project	O
,	O
which	O
is	O
still	O
available	O
for	O
backward	O
compatibility	O
.	O
</s>
<s>
BioJava	B-Language
5	O
introduced	O
new	O
features	O
to	O
two	O
modules	O
,	O
biojava-alignment	O
and	O
biojava-structure	O
.	O
</s>
<s>
some	O
of	O
the	O
new	O
features	O
that	O
are	O
included	O
in	O
the	O
latest	O
version	O
of	O
BioJava	B-Language
.	O
</s>
<s>
This	O
module	O
provides	O
Java	B-Language
classes	O
to	O
model	O
amino	O
acid	O
or	O
nucleotide	O
sequences	O
.	O
</s>
<s>
A	O
major	O
change	O
between	O
the	O
legacy	O
BioJava	B-Language
project	O
and	O
BioJava3	O
lies	O
in	O
the	O
way	O
framework	O
has	O
been	O
designed	O
to	O
exploit	O
then-new	O
innovations	O
in	O
Java	B-Language
.	O
</s>
<s>
A	O
sequence	O
is	O
defined	O
as	O
a	O
generic	O
interface	O
allowing	O
the	O
rest	B-Protocol
of	O
the	O
modules	O
to	O
create	O
any	O
utility	O
that	O
operates	O
on	O
all	O
sequences	O
.	O
</s>
<s>
The	O
following	O
algorithms	O
have	O
been	O
implemented	O
and	O
included	O
in	O
BioJava	B-Language
.	O
</s>
<s>
This	O
module	O
contains	O
several	O
classes	O
and	O
methods	O
that	O
allow	O
users	O
to	O
perform	O
pairwise	O
and	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
.	O
</s>
<s>
BioJava	B-Language
implements	O
the	O
Needleman-Wunsch	B-Algorithm
algorithm	I-Algorithm
for	O
optimal	O
global	O
alignments	O
and	O
the	O
Smith	B-Algorithm
and	I-Algorithm
Waterman	I-Algorithm
's	I-Algorithm
algorithm	O
for	O
local	B-Algorithm
alignments	I-Algorithm
.	O
</s>
<s>
In	O
addition	O
to	O
these	O
two	O
algorithms	O
,	O
there	O
is	O
an	O
implementation	O
of	O
Guan	O
–	O
Uberbacher	O
algorithm	O
which	O
performs	O
global	O
sequence	B-Algorithm
alignment	I-Algorithm
very	O
efficiently	O
since	O
it	O
only	O
uses	O
linear	O
memory	O
.	O
</s>
<s>
For	O
Multiple	O
Sequence	B-Algorithm
Alignment	I-Algorithm
,	O
any	O
of	O
the	O
methods	O
discussed	O
above	O
can	O
be	O
used	O
to	O
progressively	O
perform	O
a	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
.	O
</s>
<s>
The	O
module	O
also	O
provides	O
an	O
API	B-Application
for	O
detecting	O
pre-	O
,	O
co-	O
,	O
and	O
post-translational	O
protein	O
modifications	O
within	O
protein	O
structures	O
.	O
</s>
<s>
There	O
also	O
exists	O
flexibility	O
to	O
define	O
new	O
amino	O
acid	O
molecules	O
with	O
their	O
molecular	O
weights	O
using	O
simple	O
XML	B-Protocol
configuration	O
files	O
.	O
</s>
<s>
BioJava	B-Language
includes	O
a	O
Java	B-Language
implementation	O
of	O
the	O
predictor	O
.	O
</s>
<s>
The	O
BioJava	B-Language
3.0.5	O
makes	O
use	O
of	O
Java	B-Language
's	O
support	O
for	O
multithreading	O
to	O
improve	O
performance	O
by	O
up	O
to	O
3.2	O
times	O
,	O
on	O
a	O
modern	O
quad-core	O
machine	O
,	O
as	O
compared	O
to	O
the	O
legacy	O
C	O
implementation	O
.	O
</s>
<s>
The	O
web	O
service	O
module	O
allows	O
bioinformatics	O
services	O
to	O
be	O
accessed	O
using	O
REST	B-Protocol
protocols	O
.	O
</s>
<s>
Similar	O
to	O
BioJava	B-Language
,	O
open-source	B-Application
software	I-Application
projects	O
such	O
as	O
BioPerl	B-Application
,	O
BioPython	B-Library
,	O
and	O
BioRuby	B-Application
all	O
provide	O
tool-kits	O
with	O
multiple	O
functionality	O
that	O
make	O
it	O
easier	O
to	O
create	O
customized	O
pipelines	O
or	O
analysis	O
.	O
</s>
<s>
All	O
of	O
these	O
APIs	B-Application
offer	O
similar	O
tools	O
so	O
on	O
what	O
criteria	O
should	O
one	O
base	O
their	O
choice	O
?	O
</s>
<s>
In	O
general	O
,	O
for	O
small	O
programs	O
(	O
<	O
500	O
lines	O
)	O
that	O
will	O
be	O
used	O
by	O
only	O
an	O
individual	O
or	O
small	O
group	O
,	O
it	O
is	O
hard	O
to	O
beat	O
Perl	B-Language
and	O
BioPerl	B-Application
.	O
</s>
<s>
For	O
beginners	O
,	O
and	O
for	O
writing	O
larger	O
programs	O
in	O
the	O
Bio	O
domain	O
,	O
especially	O
those	O
to	O
be	O
shared	O
and	O
supported	O
by	O
others	O
,	O
Python	B-Language
’s	I-Language
clarity	O
and	O
brevity	O
make	O
it	O
very	O
attractive	O
.	O
</s>
<s>
For	O
those	O
who	O
might	O
be	O
leaning	O
towards	O
a	O
career	O
in	O
bioinformatics	O
and	O
who	O
want	O
to	O
learn	O
only	O
one	O
language	O
,	O
Java	B-Language
has	O
the	O
widest	O
general	O
programming	O
support	O
,	O
very	O
good	O
support	O
in	O
the	O
Bio	O
domain	O
with	O
BioJava	B-Language
,	O
and	O
is	O
now	O
the	O
de	O
facto	O
language	O
of	O
business	O
(	O
the	O
new	O
COBOL	O
,	O
for	O
better	O
or	O
worse	O
)	O
.	O
</s>
<s>
Apart	O
from	O
these	O
Bio*	O
projects	O
there	O
is	O
another	O
project	O
called	O
STRAP	O
which	O
uses	O
Java	B-Language
and	O
aims	O
for	O
similar	O
goals	O
.	O
</s>
<s>
The	O
STRAP-toolbox	O
,	O
similar	O
to	O
BioJava	B-Language
is	O
also	O
a	O
Java-toolkit	O
for	O
the	O
design	O
of	O
Bioinformatics	O
programs	O
and	O
scripts	O
.	O
</s>
<s>
The	O
similarities	O
and	O
differences	O
between	O
BioJava	B-Language
and	O
STRAP	O
are	O
as	O
follows	O
:	O
</s>
<s>
Both	O
are	O
used	O
by	O
Java	B-Language
programmers	O
to	O
code	O
bioinformatics	O
algorithms	O
.	O
</s>
<s>
Both	O
separate	O
implementations	O
and	O
definitions	O
by	O
using	O
java	B-Language
interfaces	O
.	O
</s>
<s>
BioJava	B-Language
is	O
applicable	O
to	O
nucleotide	O
and	O
peptide	O
sequences	O
and	O
can	O
be	O
applied	O
for	O
entire	O
genomes	O
.	O
</s>
<s>
BioJava	B-Language
is	O
used	O
where	O
speed	O
is	O
less	O
critical	O
.	O
</s>
<s>
BioJava	B-Language
is	O
well	O
designed	O
in	O
terms	O
of	O
type	O
safety	O
,	O
ontology	O
and	O
object	O
design	O
.	O
</s>
<s>
BioJava	B-Language
uses	O
objects	O
for	O
sequences	O
,	O
annotations	O
and	O
sequence	O
positions	O
.	O
</s>
<s>
In	O
BioJava	B-Language
peptide	O
sequences	O
and	O
nucleotide	O
sequences	O
are	O
lists	O
of	O
symbols	O
.	O
</s>
<s>
In	O
BioJava	B-Language
sequence	O
positions	O
are	O
realized	O
by	O
the	O
class	O
Location	O
.	O
</s>
<s>
BioJava	B-Language
throws	O
exceptions	O
when	O
methods	O
are	O
invoked	O
with	O
invalid	O
parameters	O
.	O
</s>
<s>
In	O
BioJava	B-Language
a	O
Sequence	O
object	O
is	O
either	O
a	O
peptide	O
sequence	O
or	O
a	O
nucleotide	O
sequence	O
.	O
</s>
<s>
The	O
following	O
projects	O
make	O
use	O
of	O
BioJava	B-Language
.	O
</s>
<s>
:	O
a	O
Dengue	O
genome	O
information	O
portal	O
that	O
uses	O
BioJava	B-Language
in	O
the	O
middleware	O
and	O
talks	O
to	O
a	O
biosql	O
database	O
.	O
</s>
<s>
:	O
A	O
BioJava	B-Language
based	O
DAS	O
server	O
.	O
</s>
<s>
BioSense	O
:	O
A	O
plug-in	B-Application
for	O
the	O
InforSense	O
Suite	O
,	O
an	O
analytics	O
software	O
platform	O
by	O
IDBS	O
that	O
unitizes	O
BioJava	B-Language
.	O
</s>
<s>
Bioclipse	B-Language
:	O
A	O
free	O
,	O
open	O
source	O
,	O
workbench	O
for	O
chemo	O
-	O
and	O
bioinformatics	O
with	O
powerful	O
editing	O
and	O
visualizing	O
abilities	O
for	O
molecules	O
,	O
sequences	O
,	O
proteins	O
,	O
spectra	O
,	O
etc	O
.	O
</s>
<s>
Uses	O
BioJava	B-Language
for	O
handling	O
most	O
input	O
data	O
formats	O
.	O
</s>
<s>
Cytoscape	B-Language
:	O
An	O
open	O
source	O
bioinformatics	O
software	O
platform	O
to	O
visualize	O
molecular	O
interaction	O
networks	O
.	O
</s>
<s>
:	O
A	O
tool	O
for	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
and	O
sequence-based	O
structure	O
alignment	O
.	O
</s>
<s>
:	O
A	O
version-aware	O
Java	B-Language
API	B-Application
to	O
Ensembl	O
data	O
systems	O
.	O
</s>
