Token	New tagger	GENIA tagger	TnT tagger	Discrepancy
PMID	NNP	NN	NNP	*
:	:	:	:
15781496	CD	CD	CD
Formation	NN	NN	NN
of	IN	IN	IN
linear	JJ	JJ	JJ
inverted	VBN	JJ	JJ	*
repeat	NN	NN	NN
amplicons	NNS	NNS	NNS
following	VBG	VBG	VBG
targeting	NN	NN	VBG	*
of	IN	IN	IN
an	DT	DT	DT
essential	JJ	JJ	JJ
gene	NN	NN	NN
in	IN	IN	IN
Leishmania	NNP	NNP	NNP
.	.	.	.
Attempts	NNS	NNS	NNS
to	TO	TO	TO
inactivate	VB	VB	VB
an	DT	DT	DT
essential	JJ	JJ	JJ
gene	NN	NN	NN
in	IN	IN	IN
the	DT	DT	DT
protozoan	NN	JJ	JJ	*
parasite	NN	NN	JJ	*
Leishmania	NNP	NNP	NNP
have	VBP	VBP	VBP
often	RB	RB	RB
led	VBN	VBD	VBN	*
to	TO	TO	TO
the	DT	DT	DT
generation	NN	NN	NN
of	IN	IN	IN
extra	JJ	JJ	JJ
copies	NNS	NNS	NNS
of	IN	IN	IN
the	DT	DT	DT
wild-type	JJ	JJ	JJ
alleles	NNS	NNS	NNS
of	IN	IN	IN
the	DT	DT	DT
gene	NN	NN	NN
.	.	.	.
In	IN	IN	IN
experiments	NNS	NNS	NNS
with	IN	IN	IN
Leishmania	NNP	NNP	NNP
tarentolae	NNP	FW	VBP	*
set	VBD	FW	VBN	*
up	RP	IN	RP	*
to	TO	TO	TO
disrupt	VB	VB	VB
the	DT	DT	DT
gene	NN	NN	NN
encoding	VBG	VBG	VBG
the	DT	DT	DT
J-binding	JJ	JJ	VBG	*
protein	NN	NN	NN
1	CD	CD	CD
(	(	(	(
JBP1	NN	NN	NNP	*
)	)	)	)
,	,	,	,
a	DT	DT	DT
protein	NN	NN	NN
binding	VBG	NN	VBG	*
to	TO	TO	TO
the	DT	DT	DT
unusual	JJ	JJ	JJ
base	NN	NN	NN
beta-D-glucosyl-hydroxymethyluracil	NN	NN	NN
(	(	(	(
J	NN	NN	NNP	*
)	)	)	)
of	IN	IN	IN
Leishmania	NNP	NNP	NNP
,	,	,	,
we	PRP	PRP	PRP
obtained	VBD	VBD	VBD
JBP1	NN	NN	JJ	*
mutants	NNS	NNS	NNS
containing	VBG	VBG	VBG
linear	JJ	JJ	JJ
DNA	NN	NN	NN
elements	NNS	NNS	NNS
(	(	(	(
amplicons	NNS	NNS	NNS
)	)	)	)
of	IN	IN	IN
approximately	RB	RB	RB
100	CD	CD	CD
kb	NN	NN	NN
.	.	.	.
These	DT	DT	DT
amplicons	NNS	NNS	NNS
consist	VBP	VBP	VBP
of	IN	IN	IN
a	DT	DT	DT
long	JJ	JJ	JJ
inverted	VBN	JJ	JJ	*
repeat	NN	NN	NN
with	IN	IN	IN
telomeric	JJ	JJ	JJ
repeats	NNS	NNS	NNS
at	IN	IN	IN
both	CC	CC	DT	*
ends	NNS	NNS	NNS
and	CC	CC	CC
contain	VBP	VBP	VBP
either	CC	CC	RB	*
the	DT	DT	DT
two	CD	CD	CD
different	JJ	JJ	JJ
targeting	VBG	NN	VBG	*
cassettes	NNS	NNS	NNS
used	VBN	VBN	VBN
to	TO	TO	TO
inactivate	VB	VB	VBP	*
JBP1	NN	NN	NNP	*
,	,	,	,
or	CC	CC	CC
one	CD	CD	CD
cassette	NN	NN	NN
and	CC	CC	CC
one	CD	CD	CD
JBP1	NN	NN	JJ	*
gene	NN	NN	NN
.	.	.	.
Each	DT	DT	DT
long	JJ	JJ	JJ
repeat	NN	NN	NN
within	IN	IN	IN
the	DT	DT	DT
linear	JJ	JJ	JJ
amplicons	NNS	NNS	NNS
corresponds	VBZ	VBZ	VBZ
to	TO	TO	TO
sequences	NNS	NNS	NNS
covering	VBG	VBG	VBG
the	DT	DT	DT
JBP1	NN	NN	JJ	*
locus	NN	NN	NNS	*
,	,	,	,
starting	VBG	VBG	VBG
at	IN	IN	IN
the	DT	DT	DT
telomeres	NNS	NNS	NNS
upstream	RB	RB	RB
of	IN	IN	IN
JBP1	NN	NN	NN
and	CC	CC	CC
ending	VBG	VBG	VBG
in	IN	IN	IN
a	DT	DT	DT
approximately	RB	RB	RB
220	CD	CD	CD
bp	NN	NN	NN
sequence	NN	NN	NN
repeated	VBN	VBN	VBN
in	IN	IN	IN
an	DT	DT	DT
inverted	JJ	JJ	JJ
(	(	(	(
palindromic	JJ	JJ	JJ
)	)	)	)
orientation	NN	NN	NN
downstream	RB	RB	JJ	*
of	IN	IN	IN
the	DT	DT	DT
JBP1	NN	NN	JJ	*
locus	NN	NN	NNS	*
.	.	.	.
We	PRP	PRP	PRP
propose	VBP	VBP	VBP
that	IN	IN	IN
these	DT	DT	DT
amplicons	NNS	NNS	NNS
have	VBP	VBP	VBP
arisen	VBN	VBN	VBN
by	IN	IN	IN
a	DT	DT	DT
template	JJ	JJ	VB	*
switch	NN	NN	NN
inside	IN	IN	IN
a	DT	DT	DT
DNA	NN	NN	NNP	*
replication	NN	NN	NN
fork	NN	NN	VB	*
involving	VBG	VBG	VBG
the	DT	DT	DT
inverted	VBN	JJ	JJ	*
DNA	NN	NN	NN
repeats	NNS	NNS	NNS
and	CC	CC	CC
helped	VBN	VBN	VBD	*
by	IN	IN	IN
the	DT	DT	DT
gene	NN	NN	NN
targeting	NN	NN	VBG	*
.	.	.	.
PMID	NNP	NN	NNP	*
:	:	:	:
15781495	CD	CD	CD
The	DT	DT	DT
genome	NN	NN	JJ	*
sequence	NN	NN	NN
of	IN	IN	IN
Salmonella	NNP	NN	NNP	*
enterica	NNP	NN	NN	*
serovar	NNP	NN	NN	*
Choleraesuis	NNP	NNP	NNP
,	,	,	,
a	DT	DT	DT
highly	RB	RB	RB
invasive	JJ	JJ	JJ
and	CC	CC	CC
resistant	JJ	JJ	JJ
zoonotic	JJ	JJ	JJ
pathogen	NN	NN	NN
.	.	.	.
Salmonella	NNP	NN	NN	*
enterica	NNP	NN	NN	*
serovar	NNP	NN	NN	*
Choleraesuis	NNP	NN	NNP	*
(	(	(	(
S.Choleraesuis	NNP	NN	NNP	*
)	)	)	)
,	,	,	,
a	DT	DT	DT
highly	RB	RB	RB
invasive	JJ	JJ	JJ
serovar	NN	NN	NN
among	IN	IN	IN
non-typhoidal	JJ	JJ	JJ
Salmonella	NNP	NN	NNP	*
,	,	,	,
usually	RB	RB	RB
causes	VBZ	VBZ	VBZ
sepsis	NN	NN	NN
or	CC	CC	CC
extra-intestinal	JJ	JJ	JJ
focal	JJ	JJ	JJ
infections	NNS	NNS	NNS
in	IN	IN	IN
humans	NNS	NNS	NNS
.	.	.	.
S.Choleraesuis	NNP	NNP	NNP
infections	NNS	NNS	NNS
have	VBP	VBP	VBP
now	RB	RB	RB
become	VBN	VBN	VB	*
particularly	RB	RB	RB
difficult	JJ	JJ	JJ
to	TO	TO	TO
treat	VB	VB	VB
because	IN	RB	IN	*
of	IN	IN	IN
the	DT	DT	DT
emergence	NN	NN	NN
of	IN	IN	IN
resistance	NN	NN	NN
to	TO	TO	TO
multiple	JJ	JJ	JJ
antimicrobial	JJ	JJ	JJ
agents	NNS	NNS	NNS
.	.	.	.
The	DT	DT	DT
4.7	CD	NN	CD	*
Mb	NN	NN	NNP	*
genome	NN	NN	JJ	*
sequence	NN	NN	NN
of	IN	IN	IN
a	DT	DT	DT
multidrug-resistant	JJ	JJ	JJ
S.Choleraesuis	NNP	NNP	NNP
strain	NN	NN	NN
SC-B67	NN	NN	NN
was	VBD	VBD	VBD
determined	VBN	VBN	VBN
.	.	.	.
Genome	NN	NN	NNP	*
wide	JJ	JJ	JJ
comparison	NN	NN	NN
of	IN	IN	IN
three	CD	CD	CD
sequenced	VBN	VBN	JJ	*
Salmonella	NNP	NN	NNP	*
genomes	NNS	NNS	NNS
revealed	VBD	VBD	VBD
that	IN	IN	IN
more	JJR	JJR	JJR
deletion	NN	NN	NN
events	NNS	NNS	NNS
occurred	VBD	VBD	VBD
in	IN	IN	IN
S.Choleraesuis	NNP	NNP	NNP
SC-B67	NN	NNP	NNP	*
and	CC	CC	CC
S.Typhi	NN	NNP	NNP	*
CT18	NN	NNP	NN	*
relative	JJ	JJ	JJ
to	TO	TO	TO
S.Typhimurium	NNP	NNP	NNP
LT2.	NNP	NNP	NNP
S.Choleraesuis	NNP	NNP	NNP
has	VBZ	VBZ	VBZ
151	CD	VBN	CD	*
pseudogenes	NNS	NNS	NNS
,	,	,	,
which	WDT	WDT	WDT
,	,	,	,
among	IN	IN	IN
the	DT	DT	DT
three	CD	CD	CD
Salmonella	NNP	NN	NNP	*
genomes	NNS	NNS	NNS
,	,	,	,
include	VBP	VBP	VBP
the	DT	DT	DT
highest	JJS	JJS	JJS
percentage	NN	NN	NN
of	IN	IN	IN
pseudogenes	NNS	NNS	NNS
arising	VBG	VBG	VBG
from	IN	IN	IN
the	DT	DT	DT
genes	NNS	NNS	NNS
involved	VBN	VBN	VBN
in	IN	IN	IN
bacterial	JJ	JJ	JJ
chemotaxis	NN	NN	NNS	*
signal-transduction	NN	NN	JJ	*
pathways	NNS	NNS	NNS
.	.	.	.
Mutations	NNS	NNS	NNS
in	IN	IN	IN
these	DT	DT	DT
genes	NNS	NNS	NNS
may	MD	MD	MD
increase	VB	VB	VB
smooth	JJ	JJ	JJ
swimming	NN	NN	NN
of	IN	IN	IN
the	DT	DT	DT
bacteria	NNS	NNS	NNS
,	,	,	,
potentially	RB	RB	RB
allowing	VBG	VBG	VBG
more	JJR	RBR	RBR	*
effective	JJ	JJ	JJ
interactions	NNS	NNS	NNS
with	IN	IN	IN
and	CC	CC	CC
invasion	NN	NN	NN
of	IN	IN	IN
host	NN	NN	NN
cells	NNS	NNS	NNS
to	TO	TO	TO
occur	VB	VB	VB
.	.	.	.
A	DT	DT	DT
key	JJ	JJ	JJ
regulatory	JJ	JJ	JJ
gene	NN	NN	NN
of	IN	IN	IN
TetR/AcrR	NN	NN	NNP	*
family	NN	NN	NN
,	,	,	,
acrR	NN	NN	NNP	*
,	,	,	,
was	VBD	VBD	VBD
inactivated	VBN	VBN	VBN
through	IN	IN	IN
the	DT	DT	DT
introduction	NN	NN	NN
of	IN	IN	IN
an	DT	DT	DT
internal	JJ	JJ	JJ
stop	NN	NN	NN
codon	NN	NN	NN
resulting	VBG	VBG	VBG
in	IN	IN	IN
overexpression	NN	NN	NN
of	IN	IN	IN
AcrAB	NN	NN	NNP	*
that	WDT	WDT	WDT
appears	VBZ	VBZ	VBZ
to	TO	TO	TO
be	VB	VB	VB
associated	VBN	VBN	VBN
with	IN	IN	IN
ciprofloxacin	NN	NN	JJ	*
resistance	NN	NN	NN
.	.	.	.
While	IN	IN	IN
lateral	JJ	JJ	JJ
gene	NN	NN	NN
transfer	NN	NN	NN
providing	VBG	VBG	VBG
basic	JJ	JJ	JJ
functions	NNS	NNS	NNS
to	TO	TO	TO
allow	VB	VB	VB
niche	NN	NN	NN
expansion	NN	NN	NN
in	IN	IN	IN
the	DT	DT	DT
host	NN	NN	NN
and	CC	CC	CC
environment	NN	NN	NN
is	VBZ	VBZ	VBZ
maintained	VBN	VBN	VBN
during	IN	IN	IN
the	DT	DT	DT
evolution	NN	NN	NN
of	IN	IN	IN
different	JJ	JJ	JJ
serovars	NNS	NNS	NNS
of	IN	IN	IN
Salmonella	NNP	NN	NNP	*
,	,	,	,
genes	NNS	NNS	NNS
providing	VBG	VBG	VBG
little	JJ	JJ	JJ
overall	JJ	JJ	JJ
selective	JJ	JJ	JJ
benefit	NN	NN	NN
may	MD	MD	MD
be	VB	VB	VB
lost	VBN	VBN	VBN
rapidly	RB	RB	RB
.	.	.	.
Our	PRP$	PRP$	PRP$
findings	NNS	NNS	NNS
suggest	VBP	VBP	VBP
that	IN	IN	IN
the	DT	DT	DT
formation	NN	NN	NN
of	IN	IN	IN
pseudogenes	NNS	NNS	NNS
may	MD	MD	MD
provide	VB	VB	VB
a	DT	DT	DT
simple	JJ	JJ	JJ
evolutionary	JJ	JJ	JJ
pathway	NN	NN	NN
that	WDT	WDT	WDT
complements	VBZ	VBZ	VBZ
gene	NN	NN	NN
acquisition	NN	NN	NN
to	TO	TO	TO
enhance	VB	VB	VB
virulence	NN	NN	NN
and	CC	CC	CC
antimicrobial	JJ	JJ	JJ
resistance	NN	NN	NN
in	IN	IN	IN
S.Choleraesuis	NNP	NNP	NNP
.	.	.	.
PMID	NNP	NN	NNP	*
:	:	:	:
15781494	CD	CD	CD
Both	CC	DT	DT	*
RNase	NN	NN	NNP	*
E	NN	NN	NNP	*
and	CC	CC	CC
RNase	NN	NN	NNP	*
III	CD	CD	NNP	*
control	NN	NN	VB	*
the	DT	DT	DT
stability	NN	NN	NN
of	IN	IN	IN
sodB	NN	NN	NNP	*
mRNA	NN	NN	NNP	*
upon	IN	IN	IN
translational	JJ	JJ	JJ
inhibition	NN	NN	NN
by	IN	IN	IN
the	DT	DT	DT
small	JJ	JJ	JJ
regulatory	JJ	JJ	JJ
RNA	NN	NN	NNP	*
RyhB	NN	NN	NNP	*
.	.	.	.
Previous	JJ	JJ	JJ
work	NN	NN	NN
has	VBZ	VBZ	VBZ
demonstrated	VBN	VBN	VBN
that	IN	IN	IN
iron-dependent	JJ	JJ	JJ
variations	NNS	NNS	NNS
in	IN	IN	IN
the	DT	DT	DT
steady-state	JJ	JJ	JJ
concentration	NN	NN	NN
and	CC	CC	CC
translatability	NN	NN	NN
of	IN	IN	IN
sodB	NN	NN	NNP	*
mRNA	NN	NN	NNP	*
are	VBP	VBP	VBP
modulated	VBN	VBN	VBN
by	IN	IN	IN
the	DT	DT	DT
small	JJ	JJ	JJ
regulatory	JJ	JJ	JJ
RNA	NN	NN	NNP	*
RyhB	NN	NN	NNP	*
,	,	,	,
the	DT	DT	DT
RNA	NN	NN	NNP	*
chaperone	NN	NN	NN
Hfq	NN	NN	NNP	*
and	CC	CC	CC
RNase	NN	NN	NNP	*
E	NN	NN	NNP	*
.	.	.	.
In	IN	IN	IN
agreement	NN	NN	NN
with	IN	IN	IN
the	DT	DT	DT
proposed	VBN	VBN	JJ	*
role	NN	NN	NN
of	IN	IN	IN
RNase	NN	NN	NNP	*
E	NN	NN	NNP	*
,	,	,	,
we	PRP	PRP	PRP
found	VBD	VBD	VBD
that	IN	IN	IN
the	DT	DT	DT
decay	NN	NN	NN
of	IN	IN	IN
sodB	NN	NN	NNP	*
mRNA	NN	NN	NNP	*
is	VBZ	VBZ	VBZ
retarded	VBN	VBN	JJ	*
upon	IN	IN	IN
inactivation	NN	NN	NN
of	IN	IN	IN
RNase	NN	NN	NNP	*
E	NN	NN	NNP	*
in	FW	FW	IN	*
vivo	FW	FW	NN	*
,	,	,	,
and	CC	CC	CC
that	IN	IN	IN
the	DT	DT	DT
enzyme	NN	NN	NN
cleaves	VBZ	VBZ	NNS	*
within	IN	IN	IN
the	DT	DT	DT
sodB	NN	NN	JJ	*
5'-untranslated	JJ	JJ	JJ
region	NN	NN	NN
(	(	(	(
5'-UTR	NN	NN	NNP	*
)	)	)	)
in	FW	FW	IN	*
vitro	FW	FW	NN	*
,	,	,	,
thereby	RB	RB	RB
removing	VBG	VBG	VBG
the	DT	DT	DT
5	CD	CD	CD
'	SYM	''	POS	*
stem-loop	NN	JJ	NN	*
structure	NN	NN	NN
that	WDT	WDT	IN	*
facilitates	VBZ	VBZ	NNS	*
Hfq	NN	NN	NNP	*
and	CC	CC	CC
ribosome	NN	NN	JJ	*
binding	NN	NN	JJ	*
.	.	.	.
Moreover	RB	RB	RB
,	,	,	,
RNase	NN	NN	NNP	*
E	NN	NN	NNP	*
cleavage	NN	NN	NN
can	MD	MD	MD
also	RB	RB	RB
occur	VB	VB	VB
at	IN	IN	IN
a	DT	DT	DT
cryptic	JJ	JJ	JJ
site	NN	NN	NN
that	WDT	WDT	WDT
becomes	VBZ	VBZ	VBZ
available	JJ	JJ	JJ
upon	IN	IN	IN
sodB	NN	NN	NNP	*
5'-UTR/RyhB	NN	CD	NNP	*
base	NN	NN	NN
pairing	NN	VBG	VBG	*
.	.	.	.
We	PRP	PRP	PRP
show	VBP	VBP	VBP
that	IN	IN	IN
while	IN	IN	IN
playing	VBG	VBG	VBG
an	DT	DT	DT
important	JJ	JJ	JJ
role	NN	NN	NN
in	IN	IN	IN
facilitating	VBG	VBG	VBG
the	DT	DT	DT
interaction	NN	NN	NN
of	IN	IN	IN
RyhB	NN	NN	NNP	*
with	IN	IN	IN
sodB	NN	NN	NNP	*
mRNA	NN	NN	NNP	*
,	,	,	,
Hfq	NN	NN	NNP	*
is	VBZ	VBZ	VBZ
not	RB	RB	RB
tightly	RB	RB	RB
retained	VBN	VBN	VBN
by	IN	IN	IN
the	DT	DT	DT
RyhB-sodB	NN	NN	NNP	*
mRNA	NN	NN	NNP	*
complex	NN	NN	NN
and	CC	CC	CC
can	MD	MD	MD
be	VB	VB	VB
released	VBN	VBN	VBN
from	IN	IN	IN
it	PRP	PRP	PRP
through	IN	IN	IN
interaction	NN	NN	NN
with	IN	IN	IN
other	JJ	JJ	JJ
RNAs	NNS	NNS	NNS
added	VBN	VBN	VBD	*
in	IN	IN	IN
trans	NNS	NNS	NNS
.	.	.	.
Unlike	IN	IN	IN
turnover	NN	NN	NN
of	IN	IN	IN
sodB	NN	NN	NNP	*
mRNA	NN	NN	NNP	*
,	,	,	,
RyhB	NN	NNP	NNP	*
decay	NN	NN	NN
in	FW	FW	IN	*
vivo	FW	FW	NN	*
is	VBZ	VBZ	VBZ
mainly	RB	RB	RB
dependent	JJ	JJ	JJ
on	IN	IN	IN
RNase	NN	NN	NNP	*
III	CD	CD	NNP	*
,	,	,	,
and	CC	CC	CC
its	PRP$	PRP$	PRP$
cleavage	NN	NN	NN
by	IN	IN	IN
RNase	NN	NN	NNP	*
III	CD	CD	NNP	*
in	FW	FW	IN	*
vitro	FW	FW	NN	*
is	VBZ	VBZ	VBZ
facilitated	VBN	VBN	VBN
upon	IN	IN	IN
base	NN	NN	NN
pairing	NN	VBG	VBG	*
with	IN	IN	IN
the	DT	DT	DT
sodB	NN	NN	JJ	*
5'-UTR	NN	NN	NN
.	.	.	.
These	DT	DT	DT
data	NNS	NNS	NNS
are	VBP	VBP	VBP
discussed	VBN	VBN	VBN
in	IN	IN	IN
terms	NNS	NNS	NNS
of	IN	IN	IN
a	DT	DT	DT
model	NN	NN	NN
,	,	,	,
which	WDT	WDT	WDT
accounts	VBZ	VBZ	VBZ
for	IN	IN	IN
the	DT	DT	DT
observed	VBN	VBN	JJ	*
roles	NNS	NNS	NNS
of	IN	IN	IN
RNase	NN	NN	NNP	*
E	NN	NN	NNP	*
and	CC	CC	CC
RNase	NN	NN	NNP	*
III	CD	CD	NNP	*
in	IN	IN	IN
sodB	NN	NN	JJ	*
mRNA	NN	NN	JJ	*
turnover	NN	NN	NN
.	.	.	.