<s>
Name	O
Description	O
Species	O
References	O
FINDER	O
Automated	O
software	O
package	O
to	O
annotate	O
eukaryotic	O
genes	O
from	O
RNA-Seq	O
data	O
and	O
associated	O
protein	O
sequences	O
Eukaryotes	O
FragGeneScan	O
Predicting	O
genes	O
in	O
complete	O
genomes	O
and	O
sequencing	O
Reads	O
Prokaryotes	O
,	O
MetagenomesATGpr	O
Identifies	O
translational	O
initiation	O
sites	O
in	O
cDNA	O
sequences	O
HumanProdigalIts	O
name	O
stands	O
for	O
Prokaryotic	O
Dynamic	B-Algorithm
Programming	I-Algorithm
Genefinding	O
Algorithm	O
.	O
</s>
<s>
It	O
is	O
based	O
on	O
log-likelihood	O
functions	O
and	O
does	O
not	O
use	O
Hidden	O
or	O
Interpolated	O
Markov	O
Models.Prokaryotes	O
,	O
Metagenomes	O
(	O
metaProdigal	O
)	O
AUGUSTUS	O
Eukaryote	O
gene	O
predictor	O
Eukaryotes	O
BGF	O
Hidden	O
Markov	O
model	O
(	O
HMM	O
)	O
and	O
dynamic	B-Algorithm
programming	I-Algorithm
based	O
ab	O
initio	O
gene	O
prediction	O
program	O
DIOGENES	O
Fast	O
detection	O
of	O
coding	O
regions	O
in	O
short	O
genome	O
sequences	O
Dragon	O
Promoter	O
Finder	O
Program	O
to	O
recognize	O
vertebrate	O
RNA	O
polymerase	O
II	O
promoters	O
Vertebrates	O
EasyGeneThe	O
gene	O
finder	O
is	O
based	O
on	O
a	O
hidden	O
Markov	O
model	O
(	O
HMM	O
)	O
that	O
is	O
automatically	O
estimated	O
for	O
a	O
new	O
genome	O
.	O
</s>
<s>
Prokaryotes	O
EuGene	O
Integrative	O
gene	O
finding	O
Prokaryotes	O
,	O
Eukaryotes	O
FGENESH	O
HMM-based	O
gene	O
structure	O
prediction	O
:	O
multiple	O
genes	O
,	O
both	O
chains	O
Eukaryotes	O
FrameD	O
Find	O
genes	O
and	O
frameshift	O
in	O
G+C	O
rich	O
prokaryote	O
sequences	O
Prokaryotes	O
,	O
Eukaryotes	O
GeMoMa	O
Homology-based	O
gene	O
prediction	O
based	O
on	O
amino	O
acid	O
and	O
intron	O
position	O
conservation	O
as	O
well	O
as	O
RNA-Seq	O
data	O
GENIUS	O
II	O
Links	O
ORFs	O
in	O
complete	O
genomes	O
to	O
protein	O
3D	O
structures	O
Prokaryotes	O
,	O
Eukaryotesgeneid	O
Program	O
to	O
predict	O
genes	O
,	O
exons	O
,	O
splice	O
sites	O
,	O
and	O
other	O
signals	O
along	O
DNA	O
sequences	O
Eukaryotes	O
GeneParser	O
Parse	O
DNA	O
sequences	O
into	O
introns	O
and	O
exons	O
Eukaryotes	O
GeneMark	B-Application
Family	O
of	O
self-training	O
gene	O
prediction	O
programs	O
Prokaryotes	O
,	O
Eukaryotes	O
,	O
</s>
<s>
Metagenomes	O
GeneTack	O
Predicts	O
genes	O
with	O
frameshifts	O
in	O
prokaryote	O
genomes	O
Prokaryotes	O
GenomeScan	O
Predicts	O
the	O
locations	O
and	O
exon-intron	O
structures	O
of	O
genes	O
in	O
genome	O
sequences	O
from	O
a	O
variety	O
of	O
organisms	O
,	O
GENSCAN	B-Application
server	O
is	O
the	O
GenomeScan	O
's	O
predecessor	O
Vertebrate	O
,	O
Arabidopsis	O
,	O
Maize	O
GENSCAN	B-Application
Predicts	O
the	O
locations	O
and	O
exon-intron	O
structures	O
of	O
genes	O
in	O
genome	O
sequences	O
from	O
a	O
variety	O
of	O
organisms	O
Vertebrate	O
,	O
Arabidopsis	O
,	O
Maize	O
GLIMMER	O
Finds	O
genes	O
in	O
microbial	O
DNA	O
Prokaryotes	O
GLIMMERHMM	O
Eukaryotic	O
gene-finding	O
system	O
Eukaryotes	O
GrailEXP	O
Predicts	O
exons	O
,	O
genes	O
,	O
promoters	O
,	O
polyas	O
,	O
CpG	O
islands	O
,	O
EST	O
similarities	O
,	O
and	O
repeat	O
elements	O
in	O
DNA	O
sequence	O
Human	O
,	O
Mus	O
musculus	O
,	O
Arabidopsis	O
thaliana	O
,	O
Drosophila	O
melanogaster	O
mGene	O
Support-vector	B-Algorithm
machine	I-Algorithm
(	O
SVM	B-Algorithm
)	O
based	O
system	O
to	O
find	O
genes	O
Eukaryotes	O
mGene.ngs	O
SVM	B-Algorithm
based	O
system	O
to	O
find	O
genes	O
using	O
heterogeneous	O
information	O
:	O
RNA-seq	O
,	O
tiling	O
arrays	O
Eukaryotes	O
MORGAN	O
Decision	O
tree	O
system	O
to	O
find	O
genes	O
in	O
vertebrate	O
DNA	O
Eukaryotes	O
BioNIX	O
Web	O
tool	O
to	O
combine	O
results	O
from	O
different	O
programs	O
:	O
GRAIL	O
,	O
FEX	O
,	O
HEXON	O
,	O
MZEF	O
,	O
GENEMARK	B-Application
,	O
GENEFINDER	O
,	O
FGENE	O
,	O
BLAST	O
,	O
POLYAH	O
,	O
REPEATMASKER	O
,	O
TRNASCAN	O
Prokaryotes	O
,	O
Eukaryotes	O
NNPP	O
Neural	B-Architecture
network	I-Architecture
promoter	O
prediction	O
Prokaryotes	O
,	O
Eukaryotes	O
NNSPLICE	O
Neural	B-Architecture
network	I-Architecture
splice	O
site	O
prediction	O
Drosophila	O
,	O
Human	O
ORFfinder	O
Graphical	O
analysis	O
tool	O
to	O
find	O
all	O
open	O
reading	O
frames	O
Prokaryotes	O
,	O
Eukaryotes	O
Regulatory	O
Sequence	O
Analysis	O
Tools	O
Series	O
of	O
modular	O
computer	O
programs	O
to	O
detect	O
regulatory	O
signals	O
in	O
non-coding	O
sequences	O
Fungi	O
,	O
Prokaryotes	O
,	O
Metazoa	O
,	O
Protist	O
,	O
Plants	O
PHANOTATE	O
A	O
tool	O
to	O
annotate	O
phage	O
genomes	O
.	O
</s>
