<s>
This	O
list	B-Application
of	I-Application
RNA	I-Application
structure	I-Application
prediction	I-Application
software	I-Application
is	O
a	O
compilation	O
of	O
software	O
tools	O
and	O
web	O
portals	O
used	O
for	O
RNA	O
structure	O
prediction	O
.	O
</s>
<s>
Links	O
References	O
CentroidFoldSecondary	O
structure	O
prediction	O
based	O
on	O
generalized	O
centroid	O
estimator	O
sourcecode	O
webserver	O
CentroidHomfoldSecondary	O
structure	O
prediction	O
by	O
using	O
homologous	O
sequence	O
information	O
sourcecode	O
webserver	O
Context	O
FoldAn	O
RNA	O
secondary	O
structure	O
prediction	O
software	O
based	O
on	O
feature-rich	B-Architecture
trained	O
scoring	O
models	O
.	O
</s>
<s>
sourcecode	O
webserver	O
CONTRAfoldSecondary	O
structure	O
prediction	O
method	O
based	O
on	O
conditional	O
log-linear	O
models	O
(	O
CLLMs	O
)	O
,	O
a	O
flexible	O
class	O
of	O
probabilistic	O
models	O
which	O
generalize	O
upon	O
SCFGs	B-General_Concept
by	O
using	O
discriminative	O
training	O
and	O
feature-rich	B-Architecture
scoring	O
.	O
</s>
<s>
webserver	O
E2EfoldA	O
deep	O
learning	O
based	O
method	O
for	O
efficiently	O
predicting	O
secondary	O
structure	O
by	O
differentiating	O
through	O
a	O
constrained	O
optimization	O
solver	O
,	O
without	O
using	O
dynamic	B-Algorithm
programming	I-Algorithm
.	O
</s>
<s>
URL	O
https://openreview.net/forum?id=S1eALyrYDH.EternaFoldA	O
multitask-learning-based	O
model	O
trained	O
on	O
data	O
from	O
the	O
Eterna	B-Application
project	O
.	O
</s>
<s>
sourcecode	O
,	O
webserver	O
pKissA	O
dynamic	B-Algorithm
programming	I-Algorithm
algorithm	O
for	O
the	O
prediction	O
of	O
a	O
restricted	O
class	O
(	O
H-type	O
and	O
kissing	O
hairpins	O
)	O
of	O
RNA	O
pseudoknots	O
.	O
</s>
<s>
sourcecode	O
,	O
webserver	O
PknotsA	O
dynamic	B-Algorithm
programming	I-Algorithm
algorithm	O
for	O
optimal	O
RNA	O
pseudoknot	O
prediction	O
using	O
the	O
nearest	O
neighbour	O
energy	O
model	O
.	O
</s>
<s>
sourcecode	O
PknotsRGA	O
dynamic	B-Algorithm
programming	I-Algorithm
algorithm	O
for	O
the	O
prediction	O
of	O
a	O
restricted	O
class	O
(	O
H-type	O
)	O
of	O
RNA	O
pseudoknots	O
.	O
</s>
<s>
sourcecode	O
,	O
webserver	O
RNA123Secondary	O
structure	O
prediction	O
via	O
thermodynamic-based	O
folding	O
algorithms	O
and	O
novel	O
structure-based	O
sequence	B-Algorithm
alignment	I-Algorithm
specific	O
for	O
RNA	O
.	O
</s>
<s>
webserver	O
RNAfold	B-Application
MFE	O
RNA	O
structure	O
prediction	O
algorithm	O
.	O
</s>
<s>
source	O
&	O
binaries	O
,	O
webserver	O
SARNA-PredictRNA	O
Secondary	O
structure	O
prediction	O
method	O
based	O
on	O
simulated	B-Algorithm
annealing	I-Algorithm
.	O
</s>
<s>
seqfold	O
is	O
an	O
implementation	O
of	O
the	O
Zuker	O
,	O
1981	O
dynamic	B-Algorithm
programming	I-Algorithm
algorithm	O
,	O
the	O
basis	O
for	O
UNAFold/mfold	O
,	O
with	O
energy	O
functions	O
from	O
SantaLucia	O
,	O
2004	O
(	O
DNA	O
)	O
and	O
Turner	O
,	O
2009	O
(	O
RNA	O
)	O
.	O
</s>
<s>
Python	B-Language
CLI	O
or	O
module	O
.	O
</s>
<s>
Links	O
References	O
BARNACLEA	O
Python	B-Language
library	O
for	O
the	O
probabilistic	O
sampling	O
of	O
RNA	O
structures	O
that	O
are	O
compatible	O
with	O
a	O
given	O
nucleotide	O
sequence	O
and	O
that	O
are	O
RNA-like	O
on	O
a	O
local	O
length	O
scale	O
.	O
</s>
<s>
sourcecode	O
,	O
webserver	O
NASTCoarse-grained	O
modeling	O
of	O
large	O
RNA	O
molecules	O
with	O
knowledge-based	O
potentials	O
and	O
structural	O
filters	O
executables	O
MMBTurning	O
limited	O
experimental	O
information	O
into	O
3D	O
models	O
of	O
RNA	O
sourcecode	O
RNA123Integrated	O
platform	O
for	O
de	O
novo	O
and	O
homology	O
modeling	O
of	O
RNA	O
3D	O
structures	O
,	O
where	O
coordinate	O
file	O
input	O
,	O
sequence	O
editing	O
,	O
sequence	B-Algorithm
alignment	I-Algorithm
,	O
structure	O
prediction	O
and	O
analysis	O
features	O
are	O
all	O
accessed	O
from	O
one	O
intuitive	O
graphical	O
user	O
interface	O
.	O
</s>
<s>
AlignmentAlignment	O
:	O
predicts	O
an	O
alignment	B-Algorithm
,	O
<input|yes|no>	O
.	O
</s>
<s>
sourcecode	O
,	O
webserver	O
,	O
website	O
CONSANimplements	O
a	O
pinned	O
Sankoff	O
algorithm	O
for	O
simultaneous	O
pairwise	O
RNA	O
alignment	B-Algorithm
and	O
consensus	O
structure	O
prediction	O
.	O
</s>
<s>
sourcecode	O
Dynalignan	O
algorithm	O
that	O
improves	O
the	O
accuracy	O
of	O
structure	O
prediction	O
by	O
combining	O
free	O
energy	O
minimization	O
and	O
comparative	O
sequence	O
analysis	O
to	O
find	O
a	O
low	O
free	O
energy	O
structure	O
common	O
to	O
two	O
sequences	O
without	O
requiring	O
any	O
sequence	B-Algorithm
identity	I-Algorithm
.	O
</s>
<s>
For	O
local	O
alignments	O
more	O
than	O
one	O
alignment	B-Algorithm
can	O
be	O
returned	O
.	O
</s>
<s>
sourcecode	O
,	O
webserver	O
,	O
website	O
FoldalignMA	O
multiple	O
RNA	O
structural	O
RNA	O
alignment	B-Algorithm
method	O
,	O
to	O
a	O
large	O
extent	O
based	O
on	O
the	O
PMcomp	O
program	O
.	O
</s>
<s>
sourcecode	O
FRUUTA	O
pairwise	O
RNA	O
structural	O
alignment	B-Algorithm
tool	O
based	O
on	O
the	O
comparison	O
of	O
RNA	O
trees	O
.	O
</s>
<s>
sourcecode	O
KNetFoldComputes	O
a	O
consensus	O
RNA	O
secondary	O
structure	O
from	O
an	O
RNA	O
sequence	B-Algorithm
alignment	I-Algorithm
based	O
on	O
machine	O
learning	O
.	O
</s>
<s>
linuxbinary	O
,	O
webserver	O
LARAProduce	O
a	O
global	O
fold	O
and	O
alignment	B-Algorithm
of	O
ncRNA	O
families	O
using	O
integer	O
linear	O
programming	O
and	O
Lagrangian	O
relaxation	O
.	O
</s>
<s>
It	O
is	O
a	O
variant	O
of	O
Sankoff	O
's	O
algorithm	O
for	O
simultaneous	O
folding	O
and	O
alignment	B-Algorithm
,	O
which	O
takes	O
as	O
input	O
pre-computed	O
base	O
pair	O
probability	O
matrices	O
from	O
McCaskill	O
's	O
algorithm	O
as	O
produced	O
by	O
RNAfold	B-Application
-p	O
.	O
Thus	O
the	O
method	O
can	O
also	O
be	O
viewed	O
as	O
way	O
to	O
compare	O
base	O
pair	O
probability	O
matrices	O
.	O
</s>
<s>
sourcecode	O
,	O
webserver	O
MASTRA	O
sampling	O
approach	O
using	O
Markov	B-General_Concept
chain	I-General_Concept
Monte	I-General_Concept
Carlo	I-General_Concept
in	O
a	O
simulated	B-Algorithm
annealing	I-Algorithm
framework	O
,	O
where	O
both	O
structure	O
and	O
alignment	B-Algorithm
is	O
optimized	O
by	O
making	O
small	O
local	O
changes	O
.	O
</s>
<s>
The	O
score	O
combines	O
the	O
log-likelihood	O
of	O
the	O
alignment	B-Algorithm
,	O
a	O
covariation	O
term	O
and	O
the	O
basepair	O
probabilities	O
.	O
</s>
<s>
It	O
does	O
not	O
require	O
any	O
sequence	B-Algorithm
identity	I-Algorithm
.	O
</s>
<s>
sourcecode	O
Murleta	O
multiple	O
alignment	B-Algorithm
tool	O
for	O
RNA	O
sequences	O
using	O
iterative	O
alignment	B-Algorithm
based	O
on	O
Sankoff	O
's	O
algorithm	O
with	O
sharply	O
reduced	O
computational	O
time	O
and	O
memory	O
.	O
</s>
<s>
webserver	O
MXSCARNAa	O
multiple	O
alignment	B-Algorithm
tool	O
for	O
RNA	O
sequences	O
using	O
progressive	O
alignment	B-Algorithm
based	O
on	O
pairwise	O
structural	O
alignment	B-Algorithm
algorithm	O
of	O
SCARNA	O
.	O
</s>
<s>
webserver	O
sourcecode	O
pAliKiss	O
pAliKiss	O
predicts	O
RNA	O
secondary	O
structures	O
for	O
fixed	O
RNA	O
multiple	O
sequence	B-Algorithm
alignments	I-Algorithm
,	O
with	O
special	O
attention	O
for	O
pseudoknotted	O
structures	O
.	O
</s>
<s>
webserver	O
sourcecode	O
PARTSA	O
method	O
for	O
joint	O
prediction	O
of	O
alignment	B-Algorithm
and	O
common	O
secondary	O
structures	O
of	O
two	O
RNA	O
sequences	O
using	O
a	O
probabilistic	O
model	O
based	O
on	O
pseudo	O
free	O
energies	O
obtained	O
from	O
precomputed	O
base	O
pairing	O
and	O
alignment	B-Algorithm
probabilities	O
.	O
</s>
<s>
The	O
structural	O
probabilities	O
are	O
calculated	O
by	O
RNAfold	B-Application
and	O
Pfold	O
.	O
</s>
<s>
sourcecode	O
PMcomp/PMmultiPMcomp	O
is	O
a	O
variant	O
of	O
Sankoff	O
's	O
algorithm	O
for	O
simultaneous	O
folding	O
and	O
alignment	B-Algorithm
,	O
which	O
takes	O
as	O
input	O
pre-computed	O
base	O
pair	O
probability	O
matrices	O
from	O
McCaskill	O
's	O
algorithm	O
as	O
produced	O
by	O
RNAfold	B-Application
-p	O
.	O
Thus	O
the	O
method	O
can	O
also	O
be	O
viewed	O
as	O
way	O
to	O
compare	O
base	O
pair	O
probability	O
matrices	O
.	O
</s>
<s>
PMmulti	O
is	O
a	O
wrapper	O
program	O
that	O
does	O
progressive	O
multiple	O
alignments	O
by	O
repeatedly	O
calling	O
pmcomp	O
sourcecode	O
,	O
webserver	O
RNAGA	O
Gibbs	O
sampling	O
method	O
to	O
determine	O
a	O
conserved	O
structure	O
and	O
the	O
structural	O
alignment	B-Algorithm
.	O
</s>
<s>
A	O
modified	O
version	O
of	O
T-Coffee	B-Application
is	O
then	O
used	O
to	O
compute	O
the	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
having	O
the	O
best	O
agreement	O
with	O
the	O
sequences	O
and	O
the	O
structures	O
.	O
</s>
<s>
R-Coffee	B-Application
can	O
be	O
combined	O
with	O
any	O
existing	O
sequence	B-Algorithm
alignment	I-Algorithm
method	O
.	O
</s>
<s>
It	O
uses	O
probabilistic	O
alignment	B-Algorithm
and	O
partition	O
functions	O
to	O
map	O
conserved	O
pairs	O
between	O
sequences	O
,	O
and	O
then	O
iterates	O
the	O
partition	O
functions	O
to	O
improve	O
structure	O
prediction	O
accuracy	O
sourcecode	O
R-scape	O
Verify	O
conserved	O
secondary	O
structure	O
by	O
measuring	O
covarying	O
basepairs	O
and	O
their	O
statistical	O
significance	O
compared	O
to	O
pure	O
phylogeny	O
.	O
</s>
<s>
home	O
page	O
RNA123Included	O
structure	O
based	O
sequence	B-Algorithm
alignment	I-Algorithm
(	O
SBSA	O
)	O
algorithm	O
uses	O
a	O
novel	O
suboptimal	O
version	O
of	O
the	O
Needleman-Wunsch	O
global	O
sequence	B-Algorithm
alignment	I-Algorithm
method	O
that	O
fully	O
accounts	O
for	O
secondary	O
structure	O
in	O
the	O
template	O
and	O
query	O
.	O
</s>
<s>
The	O
SBSA	O
algorithm	O
provides	O
>90	O
%	O
accurate	O
sequence	B-Algorithm
alignments	I-Algorithm
even	O
for	O
structures	O
as	O
large	O
as	O
bacterial	O
23S	O
rRNA	O
:	O
~	O
2,800	O
nts	O
.	O
</s>
<s>
Ships	O
with	O
the	O
ViennaRNA	B-Application
Package	I-Application
.	O
</s>
<s>
sourcecode	O
,	O
webserver	O
RNAforesterCompare	O
and	O
align	O
RNA	O
secondary	O
structures	O
via	O
a	O
"	O
forest	O
alignment	B-Algorithm
"	O
approach	O
.	O
</s>
<s>
webserver	O
RNASamplerA	O
probabilistic	O
sampling	O
approach	O
that	O
combines	O
intrasequence	O
base	O
pairing	O
probabilities	O
with	O
intersequence	O
base	O
alignment	B-Algorithm
probabilities	O
.	O
</s>
<s>
sourcecode	O
SCARNAStem	O
Candidate	O
Aligner	O
for	O
RNA	O
(	O
Scarna	O
)	O
is	O
a	O
fast	O
,	O
convenient	O
tool	O
for	O
structural	O
alignment	B-Algorithm
of	O
a	O
pair	O
of	O
RNA	O
sequences	O
.	O
</s>
<s>
sourcecode	O
Stemloca	O
program	O
for	O
pairwise	O
RNA	O
structural	O
alignment	B-Algorithm
based	O
on	O
probabilistic	O
models	O
of	O
RNA	O
structure	O
known	O
as	O
Pair	O
stochastic	B-General_Concept
context-free	I-General_Concept
grammars	I-General_Concept
.	O
</s>
<s>
sourcecode	O
StrAlan	O
alignment	B-Algorithm
tool	O
designed	O
to	O
provide	O
multiple	O
alignments	O
of	O
non-coding	O
RNAs	O
following	O
a	O
fast	O
progressive	O
strategy	O
.	O
</s>
<s>
It	O
combines	O
the	O
thermodynamic	O
base	O
pairing	O
information	O
derived	O
from	O
RNAfold	B-Application
calculations	O
in	O
the	O
form	O
of	O
base	O
pairing	O
probability	O
vectors	O
with	O
the	O
information	O
of	O
the	O
primary	O
sequence	O
.	O
</s>
<s>
It	O
takes	O
in	O
input	O
an	O
alignment	B-Algorithm
of	O
RNA	O
sequences	O
and	O
returns	O
the	O
predicted	O
secondary	O
structure(s )	O
.	O
</s>
<s>
webserver	O
WARa	O
webserver	O
that	O
makes	O
it	O
possible	O
to	O
simultaneously	O
use	O
a	O
number	O
of	O
state	O
of	O
the	O
art	O
methods	O
for	O
performing	O
multiple	O
alignment	B-Algorithm
and	O
secondary	O
structure	O
prediction	O
for	O
noncoding	O
RNA	O
sequences	O
.	O
</s>
<s>
webserver	O
Xratea	O
program	O
for	O
analysis	O
of	O
multiple	O
sequence	B-Algorithm
alignments	I-Algorithm
using	O
phylogenetic	O
grammars	O
,	O
that	O
may	O
be	O
viewed	O
as	O
a	O
flexible	O
generalization	O
of	O
the	O
"	O
Pfold	O
"	O
program	O
.	O
</s>
<s>
sourcecodeAlifreefold/AlifreefoldMultian	O
alignment-free	O
approach	O
to	O
predict	O
secondary	O
structure	O
from	O
homologous	O
RNA	O
sequences	O
.	O
</s>
<s>
(	O
2019	O
)	O
RNAsol	O
predictor	O
uses	O
a	O
unidirectional	O
LSTM	O
deep	O
learning	O
algorithm	O
with	O
evolutionary	O
information	O
generated	O
from	O
BLASTN	O
+	O
INFERNAL	O
and	O
predicted	O
secondary	O
structure	O
from	O
RNAfold	B-Application
as	O
an	O
input	O
for	O
the	O
prediction	O
of	O
RNA	O
solvent	O
accessibility	O
.	O
</s>
<s>
Name	O
Description	O
Intra-molecular	O
structure	O
Comparative	O
Link	O
References	O
RNApredator	O
RNApredator	O
uses	O
a	O
dynamic	B-Algorithm
programming	I-Algorithm
approach	O
to	O
compute	O
RNA-RNA	O
interaction	O
sites	O
.	O
</s>
<s>
sourcecode	O
webserver	O
NUPACK	B-Application
Computes	O
the	O
full	O
unpseudoknotted	O
partition	O
function	O
of	O
interacting	O
strands	O
in	O
dilute	O
solution	O
.	O
</s>
<s>
NUPACK	B-Application
OligoWalk/RNAstructurePredicts	O
bimolecular	O
secondary	O
structures	O
with	O
and	O
without	O
intramolecular	O
structure	O
.	O
</s>
<s>
sourcecode	O
webserver	O
RNAaliduplexBased	O
on	O
RNAduplex	O
with	O
bonuses	O
for	O
covarying	O
sites	O
sourcecode	O
RNAcofoldWorks	O
much	O
like	O
RNAfold	B-Application
,	O
but	O
allows	O
specifying	O
two	O
RNA	O
sequences	O
which	O
are	O
then	O
allowed	O
to	O
form	O
a	O
dimer	O
structure	O
.	O
</s>
<s>
It	O
first	O
time	O
employed	O
power	O
of	O
machine	O
learning	O
approach	O
with	O
scoring	O
scheme	O
through	O
support	O
vector	O
regression	O
(	O
SVR	O
)	O
while	O
considering	O
structural	O
and	O
alignment	B-Algorithm
aspects	O
of	O
targeting	O
in	O
plants	O
with	O
plant	O
specific	O
models	O
.	O
</s>
<s>
AlignmentAlignment	O
:	O
predicts	O
an	O
alignment	B-Algorithm
,	O
<input|yes|no>	O
.	O
</s>
<s>
Link	O
References	O
AlifoldzAssessing	O
a	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
for	O
the	O
existence	O
of	O
an	O
unusual	O
stable	O
and	O
conserved	O
RNA	O
secondary	O
structure	O
.	O
</s>
<s>
Predicted	O
structural	O
clusters	O
are	O
presented	O
as	O
alignment	B-Algorithm
.	O
</s>
<s>
sourcecode	O
MSARiheuristic	O
search	O
for	O
statistically	O
significant	O
conservation	O
of	O
RNA	O
secondary	O
structure	O
in	O
deep	O
multiple	O
sequence	B-Algorithm
alignments	I-Algorithm
.	O
</s>
<s>
sourcecode	O
RNAzprogram	O
for	O
predicting	O
structurally	O
conserved	O
and	O
thermodynamic	O
stable	O
RNA	O
secondary	O
structures	O
in	O
multiple	O
sequence	B-Algorithm
alignments	I-Algorithm
.	O
</s>
<s>
sourcecode	O
webserver	O
Xratea	O
program	O
for	O
analysis	O
of	O
multiple	O
sequence	B-Algorithm
alignments	I-Algorithm
using	O
phylogenetic	O
grammars	O
,	O
that	O
may	O
be	O
viewed	O
as	O
a	O
flexible	O
generalization	O
of	O
the	O
"	O
Evofold	O
"	O
program	O
.	O
</s>
<s>
mature	O
miRNA	O
webserver/source	O
webserver/source	O
miRNAminerGiven	O
a	O
search	O
query	O
,	O
candidate	O
homologs	O
are	O
identified	O
using	O
BLAST	O
search	O
and	O
then	O
tested	O
for	O
their	O
known	O
miRNA	O
properties	O
,	O
such	O
as	O
secondary	O
structure	O
,	O
energy	O
,	O
alignment	B-Algorithm
and	O
conservation	O
,	O
in	O
order	O
to	O
assess	O
their	O
fidelity	O
.	O
</s>
<s>
Mature	O
miRNA	O
webserver	O
RNAmicroA	O
SVM-based	O
approach	O
that	O
,	O
in	O
conjunction	O
with	O
a	O
non-stringent	O
filter	O
for	O
consensus	O
secondary	O
structures	O
,	O
is	O
capable	O
of	O
recognizing	O
microRNA	O
precursors	O
in	O
multiple	O
sequence	B-Algorithm
alignments	I-Algorithm
.	O
</s>
<s>
MicroRNA	O
homepage	O
RNAmmerRNAmmer	O
uses	O
HMMER	B-Language
to	O
annotate	O
rRNA	O
genes	O
in	O
genome	O
sequences	O
.	O
</s>
<s>
Name	O
Description	O
Link	O
References	O
DECIPHER	B-Application
(	O
software	O
)	O
FindNonCoding	O
takes	O
a	O
pattern	O
mining	O
approach	O
to	O
capture	O
the	O
essential	O
sequence	O
motifs	O
and	O
hairpin	O
loops	O
representing	O
a	O
non-coding	O
RNA	O
family	O
and	O
quickly	O
identify	O
matches	O
in	O
genomes	O
.	O
</s>
<s>
sourcecode	O
ERPIN	O
"	O
Easy	O
RNA	O
Profile	O
IdentificatioN	O
"	O
is	O
an	O
RNA	O
motif	O
search	O
program	O
reads	O
a	O
sequence	B-Algorithm
alignment	I-Algorithm
and	O
secondary	O
structure	O
,	O
and	O
automatically	O
infers	O
a	O
statistical	O
"	O
secondary	O
structure	O
profile	O
"	O
(	O
SSP	O
)	O
.	O
</s>
<s>
An	O
original	O
Dynamic	B-Algorithm
Programming	I-Algorithm
algorithm	O
then	O
matches	O
this	O
SSP	O
onto	O
any	O
target	O
database	O
,	O
finding	O
solutions	O
and	O
their	O
associated	O
scores	O
.	O
</s>
<s>
sourcecode	O
webserver	O
Infernal	O
"	O
INFERence	O
of	O
RNA	O
ALignment	B-Algorithm
"	O
is	O
for	O
searching	O
DNA	O
sequence	O
databases	O
for	O
RNA	O
structure	O
and	O
sequence	O
similarities	O
.	O
</s>
<s>
It	O
is	O
an	O
implementation	O
of	O
a	O
special	O
case	O
of	O
profile	O
stochastic	B-General_Concept
context-free	I-General_Concept
grammars	I-General_Concept
called	O
covariance	O
models	O
(	O
CMs	O
)	O
.	O
</s>
<s>
Predicted	O
structural	O
clusters	O
are	O
presented	O
as	O
alignment	B-Algorithm
.	O
</s>
<s>
sourcecode	O
RSEARCHTakes	O
one	O
RNA	O
sequence	O
with	O
its	O
secondary	O
structure	O
and	O
uses	O
a	O
local	O
alignment	B-Algorithm
algorithm	O
to	O
search	O
a	O
database	O
for	O
homologous	O
RNAs	O
.	O
</s>
<s>
AlignmentAlignment	O
:	O
benchmarks	O
alignment	B-Algorithm
tools	O
<yes|no>	O
.	O
</s>
<s>
Name	O
Description	O
AlignmentAlignment	O
:	O
view	O
and	O
edit	O
an	O
alignment	B-Algorithm
,	O
<yes|no>	O
.	O
</s>
<s>
Link	O
References	O
4saleA	O
tool	O
for	O
Synchronous	O
RNA	O
Sequence	O
and	O
Secondary	O
Structure	O
Alignment	B-Algorithm
and	O
Editing	O
sourcecode	O
Colorstock	O
,	O
SScolor	O
,	O
RatonColorstock	O
,	O
a	O
command-line	O
script	O
using	O
ANSI	O
terminal	O
color	O
;	O
SScolor	O
,	O
a	O
Perl	B-Language
script	O
that	O
generates	O
static	O
HTML	O
pages	O
;	O
and	O
Raton	O
,	O
an	O
Ajax	B-General_Concept
web	O
application	O
generating	O
dynamic	O
HTML	O
.	O
</s>
<s>
sourcecode	O
Integrated	B-Application
Genome	I-Application
Browser	I-Application
(	O
IGB	O
)	O
Multiple	O
alignment	B-Algorithm
viewer	O
written	O
in	O
Java	B-Language
.	O
</s>
<s>
sourcecode	O
JalviewMultiple	O
alignment	B-Algorithm
editor	O
written	O
in	O
Java	B-Language
.	O
</s>
<s>
sourcecode	O
RALEEa	O
major	O
mode	O
for	O
the	O
Emacs	B-Application
text	O
editor	O
.	O
</s>
<s>
It	O
provides	O
functionality	O
to	O
aid	O
the	O
viewing	O
and	O
editing	O
of	O
multiple	O
sequence	B-Algorithm
alignments	I-Algorithm
of	O
structured	O
RNAs	O
.	O
</s>
<s>
Name	O
Description	O
Link	O
References	O
Single	O
state	O
design	O
EteRNA/EteRNABotAn	O
RNA	O
folding	O
game	O
that	O
challenges	O
players	O
to	O
make	O
sequences	O
that	O
fold	O
into	O
a	O
target	O
RNA	O
structure	O
.	O
</s>
<s>
EteRNABot	O
is	O
a	O
software	O
implementation	O
based	O
on	O
design	O
rules	O
submitted	O
by	O
EteRNA	B-Application
players	O
.	O
</s>
<s>
EteRNA	B-Application
Game	O
EteRNABot	O
web	O
server	O
RNAinverse	O
The	O
ViennaRNA	B-Application
Package	I-Application
provides	O
RNAinverse	O
,	O
an	O
algorithm	O
for	O
designing	O
sequences	O
with	O
desired	O
structure	O
.	O
</s>
<s>
Web	O
Server	O
RNAiFold	O
A	O
complete	O
RNA	O
inverse	O
folding	O
approach	O
based	O
on	O
constraint	B-Application
programming	I-Application
and	O
implemented	O
using	O
OR	O
Tools	O
which	O
allows	O
for	O
the	O
specification	O
of	O
a	O
wide	O
range	O
of	O
design	O
constraints	O
.	O
</s>
<s>
The	O
RNAiFold	O
software	O
provides	O
two	O
algorithms	O
to	O
solve	O
the	O
inverse	O
folding	O
problem	O
:	O
i	O
)	O
RNA-CPdesign	O
explores	O
the	O
complete	O
search	O
space	O
and	O
ii	O
)	O
RNA-LNSdesign	O
based	O
on	O
the	O
large	B-Algorithm
neighborhood	I-Algorithm
search	I-Algorithm
metaheuristic	B-Algorithm
is	O
suitable	O
to	O
design	O
large	O
structures	O
.	O
</s>
<s>
The	O
software	O
can	O
also	O
design	O
interacting	O
RNA	O
molecules	O
using	O
RNAcofold	O
of	O
the	O
ViennaRNA	B-Application
Package	I-Application
.	O
</s>
<s>
RNA-SSD	O
is	O
publicly	O
available	O
under	O
the	O
name	O
of	O
RNA	O
Designer	O
at	O
the	O
RNASoft	O
web	O
page	O
Web	O
Server	O
INFO-RNA	O
INFO-RNA	O
uses	O
a	O
dynamic	B-Algorithm
programming	I-Algorithm
approach	O
to	O
generate	O
an	O
energy	O
optimized	O
starting	O
sequence	O
that	O
is	O
subsequently	O
further	O
improved	O
by	O
a	O
stochastic	O
local	O
search	O
that	O
uses	O
an	O
effective	O
neighbor	O
selection	O
method	O
.	O
</s>
<s>
Source	O
Code	O
IncaRNAtion	O
Successor	O
of	O
RNA-ensign	O
that	O
can	O
specifically	O
design	O
sequences	O
with	O
a	O
specified	O
GC	O
content	O
using	O
a	O
GC-weighted	O
Boltzmann	O
ensemble	O
and	O
stochastic	O
backtracking	B-Algorithm
Source	O
Code	O
DSS-Opt	O
Dynamics	O
in	O
Sequence	O
Space	O
Optimization	O
(	O
DSS-Opt	O
)	O
uses	O
Newtonian	O
dynamics	O
in	O
the	O
sequence	O
space	O
,	O
with	O
a	O
negative	O
design	O
term	O
and	O
simulated	B-Algorithm
annealing	I-Algorithm
to	O
optimize	O
a	O
sequence	O
such	O
that	O
it	O
folds	O
into	O
the	O
desired	O
secondary	O
structure	O
.	O
</s>
<s>
Due	O
to	O
the	O
flexible	O
evaluation	O
of	O
the	O
intermediate	O
sequences	O
using	O
underlying	O
programs	O
such	O
as	O
RNAfold	B-Application
,	O
pKiss	O
,	O
or	O
also	O
HotKnots	O
and	O
IPKnot	O
,	O
RNA	O
secondary	O
nested	O
structures	O
and	O
also	O
pseudoknot	O
structures	O
of	O
H	O
-	O
and	O
K-type	O
are	O
feasible	O
to	O
solve	O
with	O
this	O
approach.Web	O
Server	O
Source	O
Code	O
Dual	O
state	O
design	O
switch.pl	O
The	O
ViennaRNA	B-Application
Package	I-Application
provides	O
a	O
Perl	B-Language
script	O
to	O
design	O
RNA	O
sequences	O
that	O
can	O
adopt	O
two	O
states	O
.	O
</s>
<s>
It	O
brings	O
a	O
SWIG	B-Application
interface	O
for	O
Perl	B-Language
and	O
Python	B-Language
which	O
allows	O
for	O
an	O
effortless	O
integration	O
into	O
various	O
tools	O
.	O
</s>
<s>
Beside	O
a	O
local	O
search	O
the	O
software	O
has	O
been	O
equipped	O
with	O
a	O
simulated	B-Algorithm
annealing	I-Algorithm
approach	O
to	O
effectively	O
search	O
for	O
good	O
solutions	O
.	O
</s>
<s>
web	O
server	O
/	O
sourcecode	O
VARNAA	O
tool	O
for	O
the	O
automated	O
drawing	O
,	O
visualization	O
and	O
annotation	O
of	O
the	O
secondary	O
structure	O
of	O
RNA	O
,	O
initially	O
designed	O
as	O
a	O
companion	O
software	O
for	O
web	O
servers	O
and	O
databases	O
webapp/sourcecode	O
fornaA	O
web	O
based	O
viewer	O
for	O
displaying	O
RNA	O
secondary	O
structures	O
using	O
the	O
force-directed	O
graph	O
layout	O
provided	O
by	O
the	O
d3.js	B-Language
visualization	O
library	O
.	O
</s>
