Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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1
INTRODUCTION
1
17
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
The enzyme responsible for the majority of polyadenylation in E.coli, poly(A)polymerase (PAP I), is encoded by the pcnB gene (17).
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
130
8,400
1
false
The enzyme responsible for the majority of polyadenylation in E.coli, poly(A)polymerase (PAP I), is encoded by the pcnB gene.
[ "17" ]
The enzyme responsible for the majority of polyadenylation in E.coli, poly(A)polymerase (PAP I), is encoded by the pcnB gene.
true
true
true
true
true
1,352
1
INTRODUCTION
1
17–19
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
The consensus idea emerging from numerous studies of pcnB mutations is that the main function of polyadenylation is to facilitate degradation of short folded RNAs such as RNA fragments produced during the processing of longer RNA molecules (17–19) and of a non-functional mutated tRNA (20).
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
290
8,401
1
false
The consensus idea emerging from numerous studies of pcnB mutations is that the main function of polyadenylation is to facilitate degradation of short folded RNAs such as RNA fragments produced during the processing of longer RNA molecules and of a non-functional mutated tRNA.
[ "17–19", "20" ]
The consensus idea emerging from numerous studies of pcnB mutations is that the main function of polyadenylation is to facilitate degradation of short folded RNAs such as RNA fragments produced during the processing of longer RNA molecules and of a non-functional mutated tRNA.
true
true
true
true
true
1,352
1
INTRODUCTION
1
21
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
This latter example suggested that poly(A)-dependent decay is involved in quality surveillance of bacterial RNA, as previously reported in yeast (21).
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
150
8,402
1
false
This latter example suggested that poly(A)-dependent decay is involved in quality surveillance of bacterial RNA, as previously reported in yeast.
[ "21" ]
This latter example suggested that poly(A)-dependent decay is involved in quality surveillance of bacterial RNA, as previously reported in yeast.
true
true
true
true
true
1,352
1
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
A special function of polyadenylation is in the control of copy number of ColEI plasmids.
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
89
8,403
0
false
A special function of polyadenylation is in the control of copy number of ColEI plasmids.
[]
A special function of polyadenylation is in the control of copy number of ColEI plasmids.
true
true
true
true
true
1,352
1
INTRODUCTION
1
22
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
The decay of the regulatory RNA I is initiated by RNase E cleavage five nucleotides from the 5β€² end, which activates very fast decay via the PAP I-PNPase pathway (22).
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
167
8,404
1
false
The decay of the regulatory RNA I is initiated by RNase E cleavage five nucleotides from the 5β€² end, which activates very fast decay via the PAP I-PNPase pathway.
[ "22" ]
The decay of the regulatory RNA I is initiated by RNase E cleavage five nucleotides from the 5β€² end, which activates very fast decay via the PAP I-PNPase pathway.
true
true
true
true
true
1,352
1
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
There are also data indicating that PAP I may control the stability of primary transcripts (23,24).
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
99
8,405
0
false
There are also data indicating that PAP I may control the stability of primary transcripts.
[ "23,24" ]
There are also data indicating that PAP I may control the stability of primary transcripts.
true
true
true
true
true
1,352
1
INTRODUCTION
1
25–27
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
For instance, mutations that inactivate RNase E-dependent decay render mRNA more sensitive to poly(A)-dependent degradation (25–27).
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
132
8,406
1
false
For instance, mutations that inactivate RNase E-dependent decay render mRNA more sensitive to poly(A)-dependent degradation.
[ "25–27" ]
For instance, mutations that inactivate RNase E-dependent decay render mRNA more sensitive to poly(A)-dependent degradation.
true
true
true
true
true
1,352
1
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
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In addition, Aiso et al.
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
24
8,407
0
false
In addition, Aiso et al.
[]
In addition, Aiso et al.
true
true
true
true
true
1,352
1
INTRODUCTION
1
24
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
showed that the pcnB mutation affected degradation of rmf mRNA in stationary phase, but this effect could be indirect as it required de novo mRNA synthesis (24).
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
161
8,408
1
false
showed that the pcnB mutation affected degradation of rmf mRNA in stationary phase, but this effect could be indirect as it required de novo mRNA synthesis.
[ "24" ]
showed that the pcnB mutation affected degradation of rmf mRNA in stationary phase, but this effect could be indirect as it required de novo mRNA synthesis.
false
true
true
true
false
1,352
1
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
However, there has been no evidence so far that polyadenylation directly controls protein levels by modulating mRNA stability.
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
126
8,409
0
false
However, there has been no evidence so far that polyadenylation directly controls protein levels by modulating mRNA stability.
[]
However, there has been no evidence so far that polyadenylation directly controls protein levels by modulating mRNA stability.
true
true
true
true
true
1,352
2
INTRODUCTION
0
null
null
17,395,638
pmid-7533264|pmid-11867541
In an attempt to identify genes whose expression is affected by mRNA polyadenylation, we compared proteins of a wild-type and PAP I-deficient strains on 1D and 2D PAGE gels (2D-gel)
null
181
8,410
0
false
null
null
In an attempt to identify genes whose expression is affected by mRNA polyadenylation, we compared proteins of a wild-type and PAP I-deficient strains on 1D and 2D PAGE gels (2D-gel)
true
true
false
true
false
1,353
2
INTRODUCTION
0
null
null
17,395,638
pmid-7533264|pmid-11867541
There were several differences and, in particular, one polypeptide; glucosamine-6-phosphate synthase (GlmS) was significantly more abundant in the mutant strain.
null
161
8,411
0
false
null
null
There were several differences and, in particular, one polypeptide; glucosamine-6-phosphate synthase (GlmS) was significantly more abundant in the mutant strain.
true
true
true
true
true
1,353
2
INTRODUCTION
0
null
null
17,395,638
pmid-7533264|pmid-11867541
In this work, we demonstrate that the overexpression of GlmS is correlated with the accumulation and stabilization of the monocistronic glmS mRNA resulting from the processing of the glmU-glmS cotranscript.
null
206
8,412
0
false
null
null
In this work, we demonstrate that the overexpression of GlmS is correlated with the accumulation and stabilization of the monocistronic glmS mRNA resulting from the processing of the glmU-glmS cotranscript.
true
true
true
true
true
1,353
0
DISCUSSION
1
37
[ "B37", "B38", "B39", "B40", "B41" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
We present here evidence that poly(A)polymerase can negatively affect gene expression.
[ "37", "38", "39", "40", "41" ]
86
8,413
0
false
We present here evidence that poly(A)polymerase can negatively affect gene expression.
[]
We present here evidence that poly(A)polymerase can negatively affect gene expression.
true
true
true
true
true
1,354
0
DISCUSSION
1
37
[ "B37", "B38", "B39", "B40", "B41" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
Previously, it was thought that the role of the poly(A)-dependent pathway was to increase the turnovers of defective tRNAs (37) and non-processed RNA precursors (38), and to clear the cell of endonucleolytically produced, tightly folded mRNA fragments resistant to further degradation by exonucleases (39,40).
[ "37", "38", "39", "40", "41" ]
309
8,414
1
false
Previously, it was thought that the role of the poly(A)-dependent pathway was to increase the turnovers of defective tRNAs and non-processed RNA precursors, and to clear the cell of endonucleolytically produced, tightly folded mRNA fragments resistant to further degradation by exonucleases.
[ "37", "38", "39,40" ]
Previously, it was thought that the role of the poly(A)-dependent pathway was to increase the turnovers of defective tRNAs and non-processed RNA precursors, and to clear the cell of endonucleolytically produced, tightly folded mRNA fragments resistant to further degradation by exonucleases.
true
true
true
true
true
1,354
0
DISCUSSION
1
37
[ "B37", "B38", "B39", "B40", "B41" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
Here, we show that overproduction of glucosamine-6P synthase, an essential enzyme in E.coli in the absence of exogenous aminosugars, occurs upon inactivation of PAP I, and that this accumulation is correlated with the accumulation of the glmS mRNA and the reduction in its decay-rate.
[ "37", "38", "39", "40", "41" ]
284
8,415
0
false
Here, we show that overproduction of glucosamine-6P synthase, an essential enzyme in E.coli in the absence of exogenous aminosugars, occurs upon inactivation of PAP I, and that this accumulation is correlated with the accumulation of the glmS mRNA and the reduction in its decay-rate.
[]
Here, we show that overproduction of glucosamine-6P synthase, an essential enzyme in E.coli in the absence of exogenous aminosugars, occurs upon inactivation of PAP I, and that this accumulation is correlated with the accumulation of the glmS mRNA and the reduction in its decay-rate.
true
true
true
true
true
1,354
0
DISCUSSION
1
37
[ "B37", "B38", "B39", "B40", "B41" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
This led us to conclude that poly(A)-dependent degradation of the functional glmS mRNA determines the yield of GlmS.
[ "37", "38", "39", "40", "41" ]
116
8,416
0
false
This led us to conclude that poly(A)-dependent degradation of the functional glmS mRNA determines the yield of GlmS.
[]
This led us to conclude that poly(A)-dependent degradation of the functional glmS mRNA determines the yield of GlmS.
true
true
true
true
true
1,354
0
DISCUSSION
1
41
[ "B37", "B38", "B39", "B40", "B41" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
In agreement with our observation, glmS ORF was recently shown, using macroarrays, to be highly polyadenylated when PAP I is overproduced (41).
[ "37", "38", "39", "40", "41" ]
143
8,417
1
false
In agreement with our observation, glmS ORF was recently shown, using macroarrays, to be highly polyadenylated when PAP I is overproduced.
[ "41" ]
In agreement with our observation, glmS ORF was recently shown, using macroarrays, to be highly polyadenylated when PAP I is overproduced.
true
true
true
true
true
1,354
0
DISCUSSION
1
37
[ "B37", "B38", "B39", "B40", "B41" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
One cannot exclude, however, that polyadenylation acts indirectly on GlmS expression, e.g.
[ "37", "38", "39", "40", "41" ]
90
8,418
0
false
One cannot exclude, however, that polyadenylation acts indirectly on GlmS expression, e.g.
[]
One cannot exclude, however, that polyadenylation acts indirectly on GlmS expression, e.g.
true
true
true
true
true
1,354
0
DISCUSSION
1
37
[ "B37", "B38", "B39", "B40", "B41" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
by modulating the stability of a small regulatory RNA or another trans-acting factor.
[ "37", "38", "39", "40", "41" ]
85
8,419
0
false
by modulating the stability of a small regulatory RNA or another trans-acting factor.
[]
by modulating the stability of a small regulatory RNA or another trans-acting factor.
false
true
true
true
false
1,354
1
DISCUSSION
1
42–45
[ "B42 B43 B44 B45" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
We also demonstrate that the glmS monocistronic mRNA, stabilized in PAP I-deficient cells, likely results from the endonucleolytic maturation of the glmUS dicistronic primary transcript.
[ "42–45" ]
186
8,420
0
false
We also demonstrate that the glmS monocistronic mRNA, stabilized in PAP I-deficient cells, likely results from the endonucleolytic maturation of the glmUS dicistronic primary transcript.
[]
We also demonstrate that the glmS monocistronic mRNA, stabilized in PAP I-deficient cells, likely results from the endonucleolytic maturation of the glmUS dicistronic primary transcript.
true
true
true
true
true
1,355
1
DISCUSSION
1
42–45
[ "B42 B43 B44 B45" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
Although the dicistronic transcript was only detected in cells lacking RNase E, the fact that the monocistronic glmS transcript is still produced in these bacteria suggests that glmUS could be processed by another enzyme.
[ "42–45" ]
221
8,421
0
false
Although the dicistronic transcript was only detected in cells lacking RNase E, the fact that the monocistronic glmS transcript is still produced in these bacteria suggests that glmUS could be processed by another enzyme.
[]
Although the dicistronic transcript was only detected in cells lacking RNase E, the fact that the monocistronic glmS transcript is still produced in these bacteria suggests that glmUS could be processed by another enzyme.
true
true
true
true
true
1,355
1
DISCUSSION
1
42–45
[ "B42 B43 B44 B45" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
The 5β€² mRNA extremity mapping just downstream of the UGA stop codon suggests that ribosome stalling could be implicated in the mechanism of glmUS RNA processing (42–45).
[ "42–45" ]
169
8,422
1
false
The 5β€² mRNA extremity mapping just downstream of the UGA stop codon suggests that ribosome stalling could be implicated in the mechanism of glmUS RNA processing.
[ "42–45" ]
The 5β€² mRNA extremity mapping just downstream of the UGA stop codon suggests that ribosome stalling could be implicated in the mechanism of glmUS RNA processing.
true
true
true
true
true
1,355
2
DISCUSSION
1
22
[ "B22", "B37" ]
17,395,638
pmid-7533264|pmid-11867541
Interestingly, in spite of the fact that the glmS and glmUS mRNAs have identical 3β€² terminal structures, we found that the primary transcript is much less sensitive to the poly(A)-assisted exonucleolytic route of decay than the monocistronic processed molecule.
[ "22", "37" ]
261
8,423
0
false
Interestingly, in spite of the fact that the glmS and glmUS mRNAs have identical 3β€² terminal structures, we found that the primary transcript is much less sensitive to the poly(A)-assisted exonucleolytic route of decay than the monocistronic processed molecule.
[]
Interestingly, in spite of the fact that the glmS and glmUS mRNAs have identical 3β€² terminal structures, we found that the primary transcript is much less sensitive to the poly(A)-assisted exonucleolytic route of decay than the monocistronic processed molecule.
true
true
true
true
true
1,356
2
DISCUSSION
1
22
[ "B22", "B37" ]
17,395,638
pmid-7533264|pmid-11867541
An important question arising is how the poly(A)-assisted machinery of decay recognizes its targets and, in the case described above, how it distinguishes the glmS monocistronic mRNA from glmUS primary transcript and other primary transcripts.
[ "22", "37" ]
243
8,424
0
false
An important question arising is how the poly(A)-assisted machinery of decay recognizes its targets and, in the case described above, how it distinguishes the glmS monocistronic mRNA from glmUS primary transcript and other primary transcripts.
[]
An important question arising is how the poly(A)-assisted machinery of decay recognizes its targets and, in the case described above, how it distinguishes the glmS monocistronic mRNA from glmUS primary transcript and other primary transcripts.
true
true
true
true
true
1,356
2
DISCUSSION
1
22
[ "B22", "B37" ]
17,395,638
pmid-7533264|pmid-11867541
The fact that the glmS and glmUS mRNA correspond to the 3β€² part of the dicistronic transcript implies that it is the nature of the 5β€² part of the RNA that determines its sensitivity to this pathway.
[ "22", "37" ]
198
8,425
0
false
The fact that the glmS and glmUS mRNA correspond to the 3β€² part of the dicistronic transcript implies that it is the nature of the 5β€² part of the RNA that determines its sensitivity to this pathway.
[]
The fact that the glmS and glmUS mRNA correspond to the 3β€² part of the dicistronic transcript implies that it is the nature of the 5β€² part of the RNA that determines its sensitivity to this pathway.
true
true
true
true
true
1,356
2
DISCUSSION
1
22
[ "B22", "B37" ]
17,395,638
pmid-7533264|pmid-11867541
One possibility is that, as described earlier for RNA I, the 5β€² monophosphorylated terminus generated by RNase E facilitates polyadenylation of the glmS mRNA and thus promotes its degradation (22).
[ "22", "37" ]
197
8,426
1
false
One possibility is that, as described earlier for RNA I, the 5β€² monophosphorylated terminus generated by RNase E facilitates polyadenylation of the glmS mRNA and thus promotes its degradation.
[ "22" ]
One possibility is that, as described earlier for RNA I, the 5β€² monophosphorylated terminus generated by RNase E facilitates polyadenylation of the glmS mRNA and thus promotes its degradation.
true
true
true
true
true
1,356
2
DISCUSSION
1
22
[ "B22", "B37" ]
17,395,638
pmid-7533264|pmid-11867541
Such a model could explain why the RNase E-processed mRNA is more sensitive to the poly(A)-dependent pathway than the primary transcript harbouring a 5β€² triphosphate extremity.
[ "22", "37" ]
176
8,427
0
false
Such a model could explain why the RNase E-processed mRNA is more sensitive to the poly(A)-dependent pathway than the primary transcript harbouring a 5β€² triphosphate extremity.
[]
Such a model could explain why the RNase E-processed mRNA is more sensitive to the poly(A)-dependent pathway than the primary transcript harbouring a 5β€² triphosphate extremity.
true
true
true
true
true
1,356
2
DISCUSSION
1
22
[ "B22", "B37" ]
17,395,638
pmid-7533264|pmid-11867541
At the moment, the mechanism by which the 5β€² end of the long 1.9-kb glmS mRNA could affect a reaction occurring at its 3β€² end is not known.
[ "22", "37" ]
139
8,428
0
false
At the moment, the mechanism by which the 5β€² end of the long 1.9-kb glmS mRNA could affect a reaction occurring at its 3β€² end is not known.
[]
At the moment, the mechanism by which the 5β€² end of the long 1.9-kb glmS mRNA could affect a reaction occurring at its 3β€² end is not known.
true
true
true
true
true
1,356
2
DISCUSSION
1
37
[ "B22", "B37" ]
17,395,638
pmid-7533264|pmid-11867541
A greater accessibility of the 3β€² end has been proposed to explain why the precursor of a mutated tRNATrp is degraded by a poly(A)-dependent pathway (37).
[ "22", "37" ]
154
8,429
1
false
A greater accessibility of the 3β€² end has been proposed to explain why the precursor of a mutated tRNATrp is degraded by a poly(A)-dependent pathway.
[ "37" ]
A greater accessibility of the 3β€² end has been proposed to explain why the precursor of a mutated tRNATrp is degraded by a poly(A)-dependent pathway.
true
true
true
true
true
1,356
2
DISCUSSION
1
22
[ "B22", "B37" ]
17,395,638
pmid-7533264|pmid-11867541
One can imagine that refolding of the glmS mRNA consecutive to the processing of the primary transcript improves accessibility of PAP I and/or exoribonucleases at its 3β€² end.
[ "22", "37" ]
174
8,430
0
false
One can imagine that refolding of the glmS mRNA consecutive to the processing of the primary transcript improves accessibility of PAP I and/or exoribonucleases at its 3β€² end.
[]
One can imagine that refolding of the glmS mRNA consecutive to the processing of the primary transcript improves accessibility of PAP I and/or exoribonucleases at its 3β€² end.
true
true
true
true
true
1,356
2
DISCUSSION
1
22
[ "B22", "B37" ]
17,395,638
pmid-7533264|pmid-11867541
It is possible, for example, that translation of glmS is coupled to that of the upstream gene glmU and that a reduction of ribosome loading of the glmS message consecutive to the removal of the upstream glmU cistron modifies the folding of the molecule.
[ "22", "37" ]
253
8,431
0
false
It is possible, for example, that translation of glmS is coupled to that of the upstream gene glmU and that a reduction of ribosome loading of the glmS message consecutive to the removal of the upstream glmU cistron modifies the folding of the molecule.
[]
It is possible, for example, that translation of glmS is coupled to that of the upstream gene glmU and that a reduction of ribosome loading of the glmS message consecutive to the removal of the upstream glmU cistron modifies the folding of the molecule.
true
true
true
true
true
1,356
3
DISCUSSION
1
46
[ "B46", "B25 B26 B27" ]
17,395,638
pmid-9790196|pmid-7732015|pmid-7534403|pmid-14622415
It is worth mentioning here that the 5β€² monophosphate extremity that may trigger the poly(A)-dependent decay of the glmS mRNA may also promote its degradation by RNase E (46).
[ "46", "25–27" ]
175
8,432
1
false
It is worth mentioning here that the 5β€² monophosphate extremity that may trigger the poly(A)-dependent decay of the glmS mRNA may also promote its degradation by RNase E.
[ "46" ]
It is worth mentioning here that the 5β€² monophosphate extremity that may trigger the poly(A)-dependent decay of the glmS mRNA may also promote its degradation by RNase E.
true
true
true
true
true
1,357
3
DISCUSSION
1
46
[ "B46", "B25 B26 B27" ]
17,395,638
pmid-9790196|pmid-7732015|pmid-7534403|pmid-14622415
The fact that the glmS mRNA accumulates in the absence of PAP I at 30Β°C, 37Β°C but not at 44Β°C is consistent with the idea that the efficiency of its degradation by RNase E increases at high temperature.
[ "46", "25–27" ]
202
8,433
0
false
The fact that the glmS mRNA accumulates in the absence of PAP I at 30Β°C, 37Β°C but not at 44Β°C is consistent with the idea that the efficiency of its degradation by RNase E increases at high temperature.
[]
The fact that the glmS mRNA accumulates in the absence of PAP I at 30Β°C, 37Β°C but not at 44Β°C is consistent with the idea that the efficiency of its degradation by RNase E increases at high temperature.
true
true
true
true
true
1,357
3
DISCUSSION
1
46
[ "B46", "B25 B26 B27" ]
17,395,638
pmid-9790196|pmid-7732015|pmid-7534403|pmid-14622415
In contrast, this observation indicates that the contribution of the poly(A)-dependent pathway to the decay of this message increases at low temperature.
[ "46", "25–27" ]
153
8,434
0
false
In contrast, this observation indicates that the contribution of the poly(A)-dependent pathway to the decay of this message increases at low temperature.
[]
In contrast, this observation indicates that the contribution of the poly(A)-dependent pathway to the decay of this message increases at low temperature.
true
true
true
true
true
1,357
3
DISCUSSION
1
46
[ "B46", "B25 B26 B27" ]
17,395,638
pmid-9790196|pmid-7732015|pmid-7534403|pmid-14622415
It therefore appears that RNase E exerts a predominant role in mRNA decay around the optimum temperature of growth and that the poly(A)-dependent degradation may substitute for RNase E at lower temperatures.
[ "46", "25–27" ]
207
8,435
0
false
It therefore appears that RNase E exerts a predominant role in mRNA decay around the optimum temperature of growth and that the poly(A)-dependent degradation may substitute for RNase E at lower temperatures.
[]
It therefore appears that RNase E exerts a predominant role in mRNA decay around the optimum temperature of growth and that the poly(A)-dependent degradation may substitute for RNase E at lower temperatures.
true
true
true
true
true
1,357
3
DISCUSSION
1
25–27
[ "B46", "B25 B26 B27" ]
17,395,638
pmid-9790196|pmid-7732015|pmid-7534403|pmid-14622415
The idea that poly(A)-dependent decay can substitute for RNase E is also supported by earlier data showing that this pathway becomes effective on mRNAs that are no longer degraded by RNase E (25–27).
[ "46", "25–27" ]
199
8,436
1
false
The idea that poly(A)-dependent decay can substitute for RNase E is also supported by earlier data showing that this pathway becomes effective on mRNAs that are no longer degraded by RNase E.
[ "25–27" ]
The idea that poly(A)-dependent decay can substitute for RNase E is also supported by earlier data showing that this pathway becomes effective on mRNAs that are no longer degraded by RNase E.
true
true
true
true
true
1,357
4
DISCUSSION
1
47
[ "B47", "B36", "B35", "B48", "B49", "B50" ]
17,395,638
pmid-3297136|pmid-8349539|pmid-7545108|pmid-9829937|pmid-12794188|pmid-15029187
GlmS catalyzes the conversion of fructose-6-phosphate into glucosamine-6-phosphate, which then undergoes sequential transformations leading to the formation of UDP-N-acetylglucosamine, the major intermediate in the biosynthesis of all amino-sugar-containing macromolecules in the cell (47).
[ "47", "36", "35", "48", "49", "50" ]
290
8,437
1
false
GlmS catalyzes the conversion of fructose-6-phosphate into glucosamine-6-phosphate, which then undergoes sequential transformations leading to the formation of UDP-N-acetylglucosamine, the major intermediate in the biosynthesis of all amino-sugar-containing macromolecules in the cell.
[ "47" ]
GlmS catalyzes the conversion of fructose-6-phosphate into glucosamine-6-phosphate, which then undergoes sequential transformations leading to the formation of UDP-N-acetylglucosamine, the major intermediate in the biosynthesis of all amino-sugar-containing macromolecules in the cell.
true
true
true
true
true
1,358
4
DISCUSSION
1
36
[ "B47", "B36", "B35", "B48", "B49", "B50" ]
17,395,638
pmid-3297136|pmid-8349539|pmid-7545108|pmid-9829937|pmid-12794188|pmid-15029187
Regulation of glmS expression occurs both at the transcriptional level (36) with NagC acting as both an activator and a repressor of the glmUS operon in E.coli (35) and at the posttranscriptional level (present work).
[ "47", "36", "35", "48", "49", "50" ]
217
8,438
1
false
Regulation of glmS expression occurs both at the transcriptional level with NagC acting as both an activator and a repressor of the glmUS operon in E.coli and at the posttranscriptional level (present work).
[ "36", "35" ]
Regulation of glmS expression occurs both at the transcriptional level with NagC acting as both an activator and a repressor of the glmUS operon in E.coli and at the posttranscriptional level (present work).
true
true
true
true
true
1,358
4
DISCUSSION
1
47
[ "B47", "B36", "B35", "B48", "B49", "B50" ]
17,395,638
pmid-3297136|pmid-8349539|pmid-7545108|pmid-9829937|pmid-12794188|pmid-15029187
Interestingly, the expression of the glmS gene of Bacillus subtilis is also subject to a regulatory mechanism involving the processing and the degradation of its mRNA.
[ "47", "36", "35", "48", "49", "50" ]
167
8,439
0
false
Interestingly, the expression of the glmS gene of Bacillus subtilis is also subject to a regulatory mechanism involving the processing and the degradation of its mRNA.
[]
Interestingly, the expression of the glmS gene of Bacillus subtilis is also subject to a regulatory mechanism involving the processing and the degradation of its mRNA.
true
true
true
true
true
1,358
4
DISCUSSION
1
47
[ "B47", "B36", "B35", "B48", "B49", "B50" ]
17,395,638
pmid-3297136|pmid-8349539|pmid-7545108|pmid-9829937|pmid-12794188|pmid-15029187
However, in these bacteria lacking orthologs of both RNase E and PAP I (48,49), an alternate strategy has emerged.
[ "47", "36", "35", "48", "49", "50" ]
114
8,440
0
false
However, in these bacteria lacking orthologs of both RNase E and PAP I, an alternate strategy has emerged.
[ "48,49" ]
However, in these bacteria lacking orthologs of both RNase E and PAP I, an alternate strategy has emerged.
true
true
true
true
true
1,358
4
DISCUSSION
1
50
[ "B47", "B36", "B35", "B48", "B49", "B50" ]
17,395,638
pmid-3297136|pmid-8349539|pmid-7545108|pmid-9829937|pmid-12794188|pmid-15029187
A new class of ribozyme that cleaves the messenger of the glmS mRNA was discovered, which is activated by GlcN6P (50).
[ "47", "36", "35", "48", "49", "50" ]
118
8,441
1
false
A new class of ribozyme that cleaves the messenger of the glmS mRNA was discovered, which is activated by GlcN6P.
[ "50" ]
A new class of ribozyme that cleaves the messenger of the glmS mRNA was discovered, which is activated by GlcN6P.
true
true
true
true
true
1,358
4
DISCUSSION
1
47
[ "B47", "B36", "B35", "B48", "B49", "B50" ]
17,395,638
pmid-3297136|pmid-8349539|pmid-7545108|pmid-9829937|pmid-12794188|pmid-15029187
In spite of some sequence homology in the glmU-glmS intergenic region in bacterial species closely related to E.coli, in-line probing did not reveal any structural changes or self-cleavage activity when the entire E.coli intergenic glmU-glmS region was incubated with either Glc6P or GlcN6P (Elaine Lee and Ron Breaker, ...
[ "47", "36", "35", "48", "49", "50" ]
344
8,442
0
false
In spite of some sequence homology in the glmU-glmS intergenic region in bacterial species closely related to E.coli, in-line probing did not reveal any structural changes or self-cleavage activity when the entire E.coli intergenic glmU-glmS region was incubated with either Glc6P or GlcN6P (Elaine Lee and Ron Breaker, ...
[]
In spite of some sequence homology in the glmU-glmS intergenic region in bacterial species closely related to E.coli, in-line probing did not reveal any structural changes or self-cleavage activity when the entire E.coli intergenic glmU-glmS region was incubated with either Glc6P or GlcN6P (Elaine Lee and Ron Breaker, ...
true
true
true
true
true
1,358
4
DISCUSSION
1
47
[ "B47", "B36", "B35", "B48", "B49", "B50" ]
17,395,638
pmid-3297136|pmid-8349539|pmid-7545108|pmid-9829937|pmid-12794188|pmid-15029187
It therefore appears that different strategies exist that allow sensitive control of glmS mRNA and hence protein levels despite the fact that the machineries of mRNA processing and degradation are very different.
[ "47", "36", "35", "48", "49", "50" ]
212
8,443
0
false
It therefore appears that different strategies exist that allow sensitive control of glmS mRNA and hence protein levels despite the fact that the machineries of mRNA processing and degradation are very different.
[]
It therefore appears that different strategies exist that allow sensitive control of glmS mRNA and hence protein levels despite the fact that the machineries of mRNA processing and degradation are very different.
true
true
true
true
true
1,358
4
DISCUSSION
1
47
[ "B47", "B36", "B35", "B48", "B49", "B50" ]
17,395,638
pmid-3297136|pmid-8349539|pmid-7545108|pmid-9829937|pmid-12794188|pmid-15029187
Such pathways may present selective advantages that could explain their conservation in Gram-positive and Gram-negative bacteria.
[ "47", "36", "35", "48", "49", "50" ]
129
8,444
0
false
Such pathways may present selective advantages that could explain their conservation in Gram-positive and Gram-negative bacteria.
[]
Such pathways may present selective advantages that could explain their conservation in Gram-positive and Gram-negative bacteria.
true
true
true
true
true
1,358
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b2", "b5", "b7", "b8", "b9", "b10", "b13" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
Biology textbooks typically use phenotypic characters to describe clades, e.g.
[ "1", "2", "3", "2", "4", "2", "5", "7", "8", "9", "10", "13" ]
78
8,445
0
false
Biology textbooks typically use phenotypic characters to describe clades, e.g.
[]
Biology textbooks typically use phenotypic characters to describe clades, e.g.
true
true
true
true
true
1,359
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b2", "b5", "b7", "b8", "b9", "b10", "b13" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
milk and hair for mammals.
[ "1", "2", "3", "2", "4", "2", "5", "7", "8", "9", "10", "13" ]
26
8,446
0
false
milk and hair for mammals.
[]
milk and hair for mammals.
false
true
true
true
false
1,359
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b2", "b5", "b7", "b8", "b9", "b10", "b13" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
Not only do these synapomorphies aid in phylogenetic inference, but they also record key innovations in the history of life, as exemplified by such famous clades as Amniota and Eutheria (placental mammals).
[ "1", "2", "3", "2", "4", "2", "5", "7", "8", "9", "10", "13" ]
206
8,447
0
false
Not only do these synapomorphies aid in phylogenetic inference, but they also record key innovations in the history of life, as exemplified by such famous clades as Amniota and Eutheria (placental mammals).
[]
Not only do these synapomorphies aid in phylogenetic inference, but they also record key innovations in the history of life, as exemplified by such famous clades as Amniota and Eutheria (placental mammals).
true
true
true
true
true
1,359
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b2", "b5", "b7", "b8", "b9", "b10", "b13" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
A number of papers have used molecular synapomorphies to weigh in on phylogenetic debates.
[ "1", "2", "3", "2", "4", "2", "5", "7", "8", "9", "10", "13" ]
90
8,448
0
false
A number of papers have used molecular synapomorphies to weigh in on phylogenetic debates.
[]
A number of papers have used molecular synapomorphies to weigh in on phylogenetic debates.
true
true
true
true
true
1,359
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b2", "b5", "b7", "b8", "b9", "b10", "b13" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
A convincing molecular synapomorphy can often resolve a phylogeny that cannot be unambiguously determined by more continuously varying characters (1).
[ "1", "2", "3", "2", "4", "2", "5", "7", "8", "9", "10", "13" ]
150
8,449
1
false
A convincing molecular synapomorphy can often resolve a phylogeny that cannot be unambiguously determined by more continuously varying characters.
[ "1" ]
A convincing molecular synapomorphy can often resolve a phylogeny that cannot be unambiguously determined by more continuously varying characters.
true
true
true
true
true
1,359
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b2", "b4", "b2", "b5", "b7", "b8", "b9", "b10", "b13" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
Moreover, characteristic proteins (2) or regulatory sequences (3)β€”i.e.
[ "1", "2", "3", "2", "4", "2", "5", "7", "8", "9", "10", "13" ]
70
8,450
1
false
Moreover, characteristic proteins or regulatory sequences β€”i.e.
[ "2", "3" ]
Moreover, characteristic proteins or regulatory sequences β€”i.e.
true
true
true
true
true
1,359
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b2", "b4", "b2", "b5", "b7", "b8", "b9", "b10", "b13" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
sequences restricted to hypothesized cladesβ€”may represent landmark evolutionary events, such as the divergence of metazoans (2) or the origin of the bilaterian body plan (4).
[ "1", "2", "3", "2", "4", "2", "5", "7", "8", "9", "10", "13" ]
174
8,451
1
false
sequences restricted to hypothesized cladesβ€”may represent landmark evolutionary events, such as the divergence of metazoans or the origin of the bilaterian body plan.
[ "2", "4" ]
sequences restricted to hypothesized cladesβ€”may represent landmark evolutionary events, such as the divergence of metazoans or the origin of the bilaterian body plan.
false
true
true
true
false
1,359
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b2", "b4", "b2", "b5", "b7", "b8", "b9", "b10", "b13" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
Characteristic proteins are currently found, with some effort, by local alignment searching each gene in each genome of interest against all other genomes (2), or by the use of predefined ortholog collections, such as the COGs database (5–7).
[ "1", "2", "3", "2", "4", "2", "5", "7", "8", "9", "10", "13" ]
242
8,452
1
false
Characteristic proteins are currently found, with some effort, by local alignment searching each gene in each genome of interest against all other genomes, or by the use of predefined ortholog collections, such as the COGs database.
[ "2", "5–7" ]
Characteristic proteins are currently found, with some effort, by local alignment searching each gene in each genome of interest against all other genomes, or by the use of predefined ortholog collections, such as the COGs database.
true
true
true
true
true
1,359
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b2", "b5", "b7", "b8", "b9", "b10", "b13" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
More subtle synapomorphies, such as insertions or deletions are found serendipitously by researchers studying specific genes (8,9), or more systematically by manual examination of multiple alignments (10–13).
[ "1", "2", "3", "2", "4", "2", "5", "7", "8", "9", "10", "13" ]
208
8,453
0
false
More subtle synapomorphies, such as insertions or deletions are found serendipitously by researchers studying specific genes, or more systematically by manual examination of multiple alignments.
[ "8,9", "10–13" ]
More subtle synapomorphies, such as insertions or deletions are found serendipitously by researchers studying specific genes, or more systematically by manual examination of multiple alignments.
true
true
true
true
true
1,359
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b2", "b4", "b2", "b5", "b7", "b8", "b9", "b10", "b13" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
As more sequence becomes available, there is a need and opportunity to further automate the search for molecular synapomorphies.
[ "1", "2", "3", "2", "4", "2", "5", "7", "8", "9", "10", "13" ]
128
8,454
0
false
As more sequence becomes available, there is a need and opportunity to further automate the search for molecular synapomorphies.
[]
As more sequence becomes available, there is a need and opportunity to further automate the search for molecular synapomorphies.
true
true
true
true
true
1,359
1
INTRODUCTION
1
14
[ "b14", "b15", "b16", "b17", "b18", "b19" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
In this paper, we report on a synapomorphy search tool, called Conserv, that takes as input two sets of genomes: those for the putative clade, or in-group, and those for an out-group.
[ "14", "15", "16", "17", "18", "19" ]
183
8,455
0
false
In this paper, we report on a synapomorphy search tool, called Conserv, that takes as input two sets of genomes: those for the putative clade, or in-group, and those for an out-group.
[]
In this paper, we report on a synapomorphy search tool, called Conserv, that takes as input two sets of genomes: those for the putative clade, or in-group, and those for an out-group.
true
true
true
true
true
1,360
1
INTRODUCTION
1
14
[ "b14", "b15", "b16", "b17", "b18", "b19" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
The types of molecular synapomorphies we consider are as follows: (i) signature genes ubiquitous and unique to the clade, (ii) large insertions or deletions (indels) present only within the clade and (iii) sequence motifs well conserved within the clade but quite different outside the clade.
[ "14", "15", "16", "17", "18", "19" ]
292
8,456
0
false
The types of molecular synapomorphies we consider are as follows: (i) signature genes ubiquitous and unique to the clade, (ii) large insertions or deletions (indels) present only within the clade and (iii) sequence motifs well conserved within the clade but quite different outside the clade.
[]
The types of molecular synapomorphies we consider are as follows: (i) signature genes ubiquitous and unique to the clade, (ii) large insertions or deletions (indels) present only within the clade and (iii) sequence motifs well conserved within the clade but quite different outside the clade.
true
true
true
true
true
1,360
1
INTRODUCTION
1
14
[ "b14", "b15", "b16", "b17", "b18", "b19" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
Type (i) is generally the rarest and type (iii) the most common, so these types are roughly ordered from strongest to weakest phylogenetic evidence.
[ "14", "15", "16", "17", "18", "19" ]
148
8,457
0
false
Type (i) is generally the rarest and type (iii) the most common, so these types are roughly ordered from strongest to weakest phylogenetic evidence.
[]
Type (i) is generally the rarest and type (iii) the most common, so these types are roughly ordered from strongest to weakest phylogenetic evidence.
true
true
true
true
true
1,360
1
INTRODUCTION
1
14
[ "b14", "b15", "b16", "b17", "b18", "b19" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
Each type includes both strong and weak examples, however, and sequence alone cannot distinguish orthologs with novel function or structure, so we somewhat arbitrarily set the boundary between types (i) and (iii) using BLAST score thresholds that varied with the probe sequence length.
[ "14", "15", "16", "17", "18", "19" ]
285
8,458
0
false
Each type includes both strong and weak examples, however, and sequence alone cannot distinguish orthologs with novel function or structure, so we somewhat arbitrarily set the boundary between types (i) and (iii) using BLAST score thresholds that varied with the probe sequence length.
[]
Each type includes both strong and weak examples, however, and sequence alone cannot distinguish orthologs with novel function or structure, so we somewhat arbitrarily set the boundary between types (i) and (iii) using BLAST score thresholds that varied with the probe sequence length.
true
true
true
true
true
1,360
1
INTRODUCTION
1
14
[ "b14", "b15", "b16", "b17", "b18", "b19" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
We do not consider other types of synapomorphies, such as gene fusions (14,15) or changes in gene order (16,17).
[ "14", "15", "16", "17", "18", "19" ]
112
8,459
0
false
We do not consider other types of synapomorphies, such as gene fusions or changes in gene order.
[ "14,15", "16,17" ]
We do not consider other types of synapomorphies, such as gene fusions or changes in gene order.
true
true
true
true
true
1,360
1
INTRODUCTION
1
14
[ "b14", "b15", "b16", "b17", "b18", "b19" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
No matter the type, synapomorphies possess the same allure.
[ "14", "15", "16", "17", "18", "19" ]
59
8,460
0
false
No matter the type, synapomorphies possess the same allure.
[]
No matter the type, synapomorphies possess the same allure.
true
true
true
true
true
1,360
1
INTRODUCTION
1
18
[ "b14", "b15", "b16", "b17", "b18", "b19" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
They represent rareβ€”possibly even uniqueβ€”events that can potentially overcome the β€˜ratio problem’ illustrated in Figure 1: clock-like evolutionary models are inherently limited in their ability to resolve a short internal branch followed by long branches to leaves (18).
[ "14", "15", "16", "17", "18", "19" ]
270
8,461
1
false
They represent rareβ€”possibly even uniqueβ€”events that can potentially overcome the β€˜ratio problem’ illustrated in Figure 1: clock-like evolutionary models are inherently limited in their ability to resolve a short internal branch followed by long branches to leaves.
[ "18" ]
They represent rareβ€”possibly even uniqueβ€”events that can potentially overcome the β€˜ratio problem’ illustrated in Figure 1: clock-like evolutionary models are inherently limited in their ability to resolve a short internal branch followed by long branches to leaves.
true
true
true
true
true
1,360
1
INTRODUCTION
1
19
[ "b14", "b15", "b16", "b17", "b18", "b19" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
Sequence characteristics with an extremely large number of character states, however, as is the case with signature genes or long indels, can theoretically still retain information (19).
[ "14", "15", "16", "17", "18", "19" ]
186
8,462
1
false
Sequence characteristics with an extremely large number of character states, however, as is the case with signature genes or long indels, can theoretically still retain information.
[ "19" ]
Sequence characteristics with an extremely large number of character states, however, as is the case with signature genes or long indels, can theoretically still retain information.
true
true
true
true
true
1,360
2
INTRODUCTION
1
20
[ "b20", "b21" ]
16,936,320
pmid-7984417|pmid-15034147|pmid-8783936|pmid-10101183|pmid-7603565|pmid-15535883
Conceptually, we can think of Conserv as performing three steps.
[ "20", "21" ]
64
8,463
0
false
Conceptually, we can think of Conserv as performing three steps.
[]
Conceptually, we can think of Conserv as performing three steps.
true
true
true
true
true
1,361
2
INTRODUCTION
1
20
[ "b20", "b21" ]
16,936,320
pmid-7984417|pmid-15034147|pmid-8783936|pmid-10101183|pmid-7603565|pmid-15535883
First it performs an all-against-all local alignment search, probing each protein-coding gene in each genome against every other genome.
[ "20", "21" ]
136
8,464
0
false
First it performs an all-against-all local alignment search, probing each protein-coding gene in each genome against every other genome.
[]
First it performs an all-against-all local alignment search, probing each protein-coding gene in each genome against every other genome.
true
true
true
true
true
1,361
2
INTRODUCTION
1
20
[ "b20", "b21" ]
16,936,320
pmid-7984417|pmid-15034147|pmid-8783936|pmid-10101183|pmid-7603565|pmid-15535883
Second, it processes the resulting sets of hits to find the orthologous families most conserved over the in-group genomes.
[ "20", "21" ]
122
8,465
0
false
Second, it processes the resulting sets of hits to find the orthologous families most conserved over the in-group genomes.
[]
Second, it processes the resulting sets of hits to find the orthologous families most conserved over the in-group genomes.
true
true
true
true
true
1,361
2
INTRODUCTION
1
20
[ "b20", "b21" ]
16,936,320
pmid-7984417|pmid-15034147|pmid-8783936|pmid-10101183|pmid-7603565|pmid-15535883
Third, it ranks the families by β€˜synaptitude’, which measures in-group pairwise similarity scores relative to in-to-out similarity scores.
[ "20", "21" ]
138
8,466
0
false
Third, it ranks the families by β€˜synaptitude’, which measures in-group pairwise similarity scores relative to in-to-out similarity scores.
[]
Third, it ranks the families by β€˜synaptitude’, which measures in-group pairwise similarity scores relative to in-to-out similarity scores.
true
true
true
true
true
1,361
2
INTRODUCTION
1
20
[ "b20", "b21" ]
16,936,320
pmid-7984417|pmid-15034147|pmid-8783936|pmid-10101183|pmid-7603565|pmid-15535883
All three types of molecular synapomorphies, (i–iii) above, show up near the top of the ranked list.
[ "20", "21" ]
100
8,467
0
false
All three types of molecular synapomorphies, (i–iii) above, show up near the top of the ranked list.
[]
All three types of molecular synapomorphies, (i–iii) above, show up near the top of the ranked list.
true
true
true
true
true
1,361
2
INTRODUCTION
1
20
[ "b20", "b21" ]
16,936,320
pmid-7984417|pmid-15034147|pmid-8783936|pmid-10101183|pmid-7603565|pmid-15535883
Evaluation of the significance of the discovered synapomorphies remains a manual (and poorly understood) process, but this step can be facilitated by existing bioinformatics tools, such as local alignment search and multiple alignment programs (20,21).
[ "20", "21" ]
252
8,468
0
false
Evaluation of the significance of the discovered synapomorphies remains a manual (and poorly understood) process, but this step can be facilitated by existing bioinformatics tools, such as local alignment search and multiple alignment programs.
[ "20,21" ]
Evaluation of the significance of the discovered synapomorphies remains a manual (and poorly understood) process, but this step can be facilitated by existing bioinformatics tools, such as local alignment search and multiple alignment programs.
true
true
true
true
true
1,361
3
INTRODUCTION
1
5
[ "b5", "b22", "b22", "b24", "b25", "b25", "b26" ]
16,936,320
pmid-12515582|NA|NA|pmid-15681613|NA|NA|pmid-9918945
We emphasize that Conserv is a search tool, and not a complete tool for inferring a phylogenetic tree or network.
[ "5", "22", "22", "24", "25", "25", "26" ]
113
8,469
0
false
We emphasize that Conserv is a search tool, and not a complete tool for inferring a phylogenetic tree or network.
[]
We emphasize that Conserv is a search tool, and not a complete tool for inferring a phylogenetic tree or network.
true
true
true
true
true
1,362
3
INTRODUCTION
1
22
[ "b5", "b22", "b22", "b24", "b25", "b25", "b26" ]
16,936,320
pmid-12515582|NA|NA|pmid-15681613|NA|NA|pmid-9918945
Conserv's candidate synapomorphies can be used in conjunction with methods, such as parsimony (5,22) or Dollo parsimony (22) to reconstruct a tree; however, because conserved genes and indels that occur in only a single putative clade are rare, Conserv is unlikely to find enough synapomorphies to reconstruct a large tr...
[ "5", "22", "22", "24", "25", "25", "26" ]
323
8,470
1
false
Conserv's candidate synapomorphies can be used in conjunction with methods, such as parsimony or Dollo parsimony to reconstruct a tree; however, because conserved genes and indels that occur in only a single putative clade are rare, Conserv is unlikely to find enough synapomorphies to reconstruct a large tree.
[ "5,22", "22" ]
Conserv's candidate synapomorphies can be used in conjunction with methods, such as parsimony or Dollo parsimony to reconstruct a tree; however, because conserved genes and indels that occur in only a single putative clade are rare, Conserv is unlikely to find enough synapomorphies to reconstruct a large tree.
true
true
true
true
true
1,362
3
INTRODUCTION
1
5
[ "b5", "b22", "b22", "b24", "b25", "b25", "b26" ]
16,936,320
pmid-12515582|NA|NA|pmid-15681613|NA|NA|pmid-9918945
In this case, the program can provide confirmatory evidence and help evaluate trees suggested by other means.
[ "5", "22", "22", "24", "25", "25", "26" ]
109
8,471
0
false
In this case, the program can provide confirmatory evidence and help evaluate trees suggested by other means.
[]
In this case, the program can provide confirmatory evidence and help evaluate trees suggested by other means.
true
true
true
true
true
1,362
3
INTRODUCTION
1
5
[ "b5", "b22", "b22", "b24", "b25", "b25", "b26" ]
16,936,320
pmid-12515582|NA|NA|pmid-15681613|NA|NA|pmid-9918945
Notice that phylogeny by synapomorphies and parsimony is quite distinct from phylogeny by gene content (24,25), as a single gene with the right distribution pattern may decide a branch, whereas such a gene counts no more heavily than one with a scattered distribution in gene-content methods.
[ "5", "22", "22", "24", "25", "25", "26" ]
292
8,472
0
false
Notice that phylogeny by synapomorphies and parsimony is quite distinct from phylogeny by gene content, as a single gene with the right distribution pattern may decide a branch, whereas such a gene counts no more heavily than one with a scattered distribution in gene-content methods.
[ "24,25" ]
Notice that phylogeny by synapomorphies and parsimony is quite distinct from phylogeny by gene content, as a single gene with the right distribution pattern may decide a branch, whereas such a gene counts no more heavily than one with a scattered distribution in gene-content methods.
true
true
true
true
true
1,362
3
INTRODUCTION
1
5
[ "b5", "b22", "b22", "b24", "b25", "b25", "b26" ]
16,936,320
pmid-12515582|NA|NA|pmid-15681613|NA|NA|pmid-9918945
Finally, it is worth reiterating that Conserv is a relatively simple tool, optimized for speed.
[ "5", "22", "22", "24", "25", "25", "26" ]
95
8,473
0
false
Finally, it is worth reiterating that Conserv is a relatively simple tool, optimized for speed.
[]
Finally, it is worth reiterating that Conserv is a relatively simple tool, optimized for speed.
true
true
true
true
true
1,362
3
INTRODUCTION
1
5
[ "b5", "b22", "b22", "b24", "b25", "b25", "b26" ]
16,936,320
pmid-12515582|NA|NA|pmid-15681613|NA|NA|pmid-9918945
Because Conserv considers only highly conserved proteins and obvious homology (at least 25% identity), and performs only pairwise alignments, it has no need for sophisticated sequence modeling techniques, such as hidden Markov models (HMMs) (25,26).
[ "5", "22", "22", "24", "25", "25", "26" ]
249
8,474
0
false
Because Conserv considers only highly conserved proteins and obvious homology, and performs only pairwise alignments, it has no need for sophisticated sequence modeling techniques, such as hidden Markov models (HMMs).
[ "at least 25% identity", "25,26" ]
Because Conserv considers only highly conserved proteins and obvious homology, and performs only pairwise alignments, it has no need for sophisticated sequence modeling techniques, such as hidden Markov models (HMMs).
true
true
true
true
true
1,362
4
INTRODUCTION
1
27
[ "b27" ]
16,936,320
pmid-15608212
Conserv is currently most useful for prokaryotic genomes.
[ "27" ]
57
8,475
0
false
Conserv is currently most useful for prokaryotic genomes.
[]
Conserv is currently most useful for prokaryotic genomes.
true
true
true
true
true
1,363
4
INTRODUCTION
1
27
[ "b27" ]
16,936,320
pmid-15608212
When run on a putative eukaryotic clade, e.g.
[ "27" ]
45
8,476
0
false
When run on a putative eukaryotic clade, e.g.
[]
When run on a putative eukaryotic clade, e.g.
true
true
true
true
true
1,363
4
INTRODUCTION
1
27
[ "b27" ]
16,936,320
pmid-15608212
Ecdysozoa, Conserv will return voluminous results that are hard to evaluate, due to the sparse and uneven taxon sampling of eukaryotes.
[ "27" ]
135
8,477
0
false
Ecdysozoa, Conserv will return voluminous results that are hard to evaluate, due to the sparse and uneven taxon sampling of eukaryotes.
[]
Ecdysozoa, Conserv will return voluminous results that are hard to evaluate, due to the sparse and uneven taxon sampling of eukaryotes.
true
true
true
true
true
1,363
4
INTRODUCTION
1
27
[ "b27" ]
16,936,320
pmid-15608212
Thus, to demonstrate the utility of Conserv, we ran the program over bacterial genomes in GenBank (27) for about 30 choices of in-groups and out-groups, both putative clades and other sets of genomes.
[ "27" ]
200
8,478
1
false
Thus, to demonstrate the utility of Conserv, we ran the program over bacterial genomes in GenBank for about 30 choices of in-groups and out-groups, both putative clades and other sets of genomes.
[ "27" ]
Thus, to demonstrate the utility of Conserv, we ran the program over bacterial genomes in GenBank for about 30 choices of in-groups and out-groups, both putative clades and other sets of genomes.
true
true
true
true
true
1,363
4
INTRODUCTION
1
27
[ "b27" ]
16,936,320
pmid-15608212
In this test, we discovered possible synapomorphies for higher-level clades uniting Planctomycetes with Chlamydiales and Chloroflexi with Cyanobacteria, as in Figure 1.
[ "27" ]
168
8,479
0
false
In this test, we discovered possible synapomorphies for higher-level clades uniting Planctomycetes with Chlamydiales and Chloroflexi with Cyanobacteria, as in Figure 1.
[]
In this test, we discovered possible synapomorphies for higher-level clades uniting Planctomycetes with Chlamydiales and Chloroflexi with Cyanobacteria, as in Figure 1.
true
true
true
true
true
1,363
4
INTRODUCTION
1
27
[ "b27" ]
16,936,320
pmid-15608212
We also discovered strong evidence for placing Symbiobacterium in Firmicutes, and weaker evidence for placing the endosymbionts Buchnera and Wigglesworthia in Enterobacteria.
[ "27" ]
174
8,480
0
false
We also discovered strong evidence for placing Symbiobacterium in Firmicutes, and weaker evidence for placing the endosymbionts Buchnera and Wigglesworthia in Enterobacteria.
[]
We also discovered strong evidence for placing Symbiobacterium in Firmicutes, and weaker evidence for placing the endosymbionts Buchnera and Wigglesworthia in Enterobacteria.
true
true
true
true
true
1,363
4
INTRODUCTION
1
27
[ "b27" ]
16,936,320
pmid-15608212
The placement of Symbiobacterium with Firmicutes contradicts the current GenBank taxonomy, which places it in Actinobacteria, yet the discovered synapomorphies seem incontrovertible.
[ "27" ]
182
8,481
0
false
The placement of Symbiobacterium with Firmicutes contradicts the current GenBank taxonomy, which places it in Actinobacteria, yet the discovered synapomorphies seem incontrovertible.
[]
The placement of Symbiobacterium with Firmicutes contradicts the current GenBank taxonomy, which places it in Actinobacteria, yet the discovered synapomorphies seem incontrovertible.
true
true
true
true
true
1,363
4
INTRODUCTION
1
27
[ "b27" ]
16,936,320
pmid-15608212
We discovered signature genes for a number of clades, including Actinobacteria and Firmicutes.
[ "27" ]
94
8,482
0
false
We discovered signature genes for a number of clades, including Actinobacteria and Firmicutes.
[]
We discovered signature genes for a number of clades, including Actinobacteria and Firmicutes.
true
true
true
true
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1,363
4
INTRODUCTION
1
27
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16,936,320
pmid-15608212
We also used Conserv to explore surprising similarities between two groups that do not together form a clade: Ι›-Proteobacteria and Spirochaetes.
[ "27" ]
144
8,483
0
false
We also used Conserv to explore surprising similarities between two groups that do not together form a clade: Ι›-Proteobacteria and Spirochaetes.
[]
We also used Conserv to explore surprising similarities between two groups that do not together form a clade: Ι›-Proteobacteria and Spirochaetes.
true
true
true
true
true
1,363
4
INTRODUCTION
1
27
[ "b27" ]
16,936,320
pmid-15608212
Finally, we used the tool to answer an intriguing peripheral question: what is the most conserved protein?
[ "27" ]
106
8,484
0
false
Finally, we used the tool to answer an intriguing peripheral question: what is the most conserved protein?
[]
Finally, we used the tool to answer an intriguing peripheral question: what is the most conserved protein?
true
true
true
true
true
1,363
0
DISCUSSION
1
10
[ "b10", "b11", "b36", "b37", "b42", "b60" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
Molecular synapomorphies are potentially very valuable phylogenetic characters, because rare discontinuous eventsβ€”a large insertion or deletion, or the β€˜sudden’ appearance of a novel, highly conserved geneβ€”are not easily erased by subsequent point mutations.
[ "10", "11", "36", "37", "42", "60" ]
258
8,485
0
false
Molecular synapomorphies are potentially very valuable phylogenetic characters, because rare discontinuous eventsβ€”a large insertion or deletion, or the β€˜sudden’ appearance of a novel, highly conserved geneβ€”are not easily erased by subsequent point mutations.
[]
Molecular synapomorphies are potentially very valuable phylogenetic characters, because rare discontinuous eventsβ€”a large insertion or deletion, or the β€˜sudden’ appearance of a novel, highly conserved geneβ€”are not easily erased by subsequent point mutations.
true
true
true
true
true
1,364
0
DISCUSSION
1
10
[ "b10", "b11", "b36", "b37", "b42", "b60" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
Moreover, molecular synapomorphies are complementary to popular sequence-based methods, such as maximum likelihood, which do not ordinarily take into account non-ubiquitous characters, such as insertions and deletions (β€˜gap columns') and proteins unique to a clade.
[ "10", "11", "36", "37", "42", "60" ]
265
8,486
0
false
Moreover, molecular synapomorphies are complementary to popular sequence-based methods, such as maximum likelihood, which do not ordinarily take into account non-ubiquitous characters, such as insertions and deletions (β€˜gap columns') and proteins unique to a clade.
[]
Moreover, molecular synapomorphies are complementary to popular sequence-based methods, such as maximum likelihood, which do not ordinarily take into account non-ubiquitous characters, such as insertions and deletions (β€˜gap columns') and proteins unique to a clade.
true
true
true
true
true
1,364
0
DISCUSSION
1
10
[ "b10", "b11", "b36", "b37", "b42", "b60" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
To date, however, molecular synapomorphies have been used on an ad hoc basis, with phylogenies inferred from a handful of manually discovered synapomorphies.
[ "10", "11", "36", "37", "42", "60" ]
157
8,487
0
false
To date, however, molecular synapomorphies have been used on an ad hoc basis, with phylogenies inferred from a handful of manually discovered synapomorphies.
[]
To date, however, molecular synapomorphies have been used on an ad hoc basis, with phylogenies inferred from a handful of manually discovered synapomorphies.
true
true
true
true
true
1,364
0
DISCUSSION
1
10
[ "b10", "b11", "b36", "b37", "b42", "b60" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
Nevertheless, the prokaryotic phylogenies computed in the 1990s by Gupta et al.
[ "10", "11", "36", "37", "42", "60" ]
79
8,488
0
false
Nevertheless, the prokaryotic phylogenies computed in the 1990s by Gupta et al.
[]
Nevertheless, the prokaryotic phylogenies computed in the 1990s by Gupta et al.
true
true
true
true
true
1,364
0
DISCUSSION
1
10
[ "b10", "b11", "b36", "b37", "b42", "b60" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
(10,11) from hand-picked indels in selected genes show broad agreement with recent phylogenies computed using complete genomes and the latest tools (36,37,42).
[ "10", "11", "36", "37", "42", "60" ]
159
8,489
0
false
from hand-picked indels in selected genes show broad agreement with recent phylogenies computed using complete genomes and the latest tools.
[ "10,11", "36,37,42" ]
from hand-picked indels in selected genes show broad agreement with recent phylogenies computed using complete genomes and the latest tools.
false
true
true
true
false
1,364
0
DISCUSSION
1
60
[ "b10", "b11", "b36", "b37", "b42", "b60" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
We do not expect molecular synapomorphies to replace modern tree-building methods, but we can imagine hybrid methods akin to those devised for gene trees (60) and routine use of synapomorphies to rescore a small number of alternative trees.
[ "10", "11", "36", "37", "42", "60" ]
240
8,490
1
false
We do not expect molecular synapomorphies to replace modern tree-building methods, but we can imagine hybrid methods akin to those devised for gene trees and routine use of synapomorphies to rescore a small number of alternative trees.
[ "60" ]
We do not expect molecular synapomorphies to replace modern tree-building methods, but we can imagine hybrid methods akin to those devised for gene trees and routine use of synapomorphies to rescore a small number of alternative trees.
true
true
true
true
true
1,364
0
DISCUSSION
1
10
[ "b10", "b11", "b36", "b37", "b42", "b60" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
Until now there has been, to our knowledge, no effort or means to automatically gather β€˜all’ synapomorphies bearing on a phylogenetic question.
[ "10", "11", "36", "37", "42", "60" ]
143
8,491
0
false
Until now there has been, to our knowledge, no effort or means to automatically gather β€˜all’ synapomorphies bearing on a phylogenetic question.
[]
Until now there has been, to our knowledge, no effort or means to automatically gather β€˜all’ synapomorphies bearing on a phylogenetic question.
true
true
true
true
true
1,364
0
DISCUSSION
1
10
[ "b10", "b11", "b36", "b37", "b42", "b60" ]
16,936,320
pmid-11050348|pmid-11591483|pmid-12823453|pmid-11591483|pmid-9733577|pmid-11591483|pmid-12515582|pmid-11125040|pmid-11470848|pmid-10606644|pmid-9841678|pmid-15179606|pmid-9841678|pmid-10361294|pmid-15535883|pmid-15927057|pmid-11734060|NA
Hence we believe that Conserv, simple as it is, can play a role in phylogenetic inference, as well as in data mining for unexpected nuggets, such as the similarity of the flagellar proteins of Ι›-Proteobacteria and Spirochaetes.
[ "10", "11", "36", "37", "42", "60" ]
227
8,492
0
false
Hence we believe that Conserv, simple as it is, can play a role in phylogenetic inference, as well as in data mining for unexpected nuggets, such as the similarity of the flagellar proteins of Ι›-Proteobacteria and Spirochaetes.
[]
Hence we believe that Conserv, simple as it is, can play a role in phylogenetic inference, as well as in data mining for unexpected nuggets, such as the similarity of the flagellar proteins of Ι›-Proteobacteria and Spirochaetes.
true
true
true
true
true
1,364
1
DISCUSSION
1
10
[ "b10", "b12" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
The sensitivity and specificity of Conserv are hard to assess at this point, as we do not have a test set of agreed-upon synapomorphies or a validated mathematical model.
[ "10", "12" ]
170
8,493
0
false
The sensitivity and specificity of Conserv are hard to assess at this point, as we do not have a test set of agreed-upon synapomorphies or a validated mathematical model.
[]
The sensitivity and specificity of Conserv are hard to assess at this point, as we do not have a test set of agreed-upon synapomorphies or a validated mathematical model.
true
true
true
true
true
1,365
1
DISCUSSION
1
10
[ "b10", "b12" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
Conserv appears to be fairly effective at finding signature-gene and motif synapomorphies, which are easy to recognize from pairwise alignments, but indel synapomorphies remain somewhat problematic.
[ "10", "12" ]
198
8,494
0
false
Conserv appears to be fairly effective at finding signature-gene and motif synapomorphies, which are easy to recognize from pairwise alignments, but indel synapomorphies remain somewhat problematic.
[]
Conserv appears to be fairly effective at finding signature-gene and motif synapomorphies, which are easy to recognize from pairwise alignments, but indel synapomorphies remain somewhat problematic.
true
true
true
true
true
1,365
1
DISCUSSION
1
10
[ "b10", "b12" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
Conserv found most of the indels manually discovered by Gupta et al.
[ "10", "12" ]
68
8,495
0
false
Conserv found most of the indels manually discovered by Gupta et al.
[]
Conserv found most of the indels manually discovered by Gupta et al.
true
true
true
true
true
1,365
1
DISCUSSION
1
10
[ "b10", "b12" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
(10–12) from multiple alignments, but missed some of the less obvious (and more arguable) one- and two-residue indels.
[ "10", "12" ]
118
8,496
0
false
from multiple alignments, but missed some of the less obvious (and more arguable) one- and two-residue indels.
[ "10–12" ]
from multiple alignments, but missed some of the less obvious (and more arguable) one- and two-residue indels.
false
true
true
true
false
1,365
1
DISCUSSION
1
10
[ "b10", "b12" ]
16,936,320
pmid-12098695|pmid-12049665|pmid-10101183|pmid-7603565|NA|NA|pmid-9841678|pmid-15239383
The great difference in the numbers of signature genes found by our study and that of Daubin and Ochman reveals that Conserv's sensitivity could be improved by a more flexible definition of synaptitude that allows signature genes to be missing from organisms deemed safely interior to the in-group.
[ "10", "12" ]
298
8,497
0
false
The great difference in the numbers of signature genes found by our study and that of Daubin and Ochman reveals that Conserv's sensitivity could be improved by a more flexible definition of synaptitude that allows signature genes to be missing from organisms deemed safely interior to the in-group.
[]
The great difference in the numbers of signature genes found by our study and that of Daubin and Ochman reveals that Conserv's sensitivity could be improved by a more flexible definition of synaptitude that allows signature genes to be missing from organisms deemed safely interior to the in-group.
true
true
true
true
true
1,365
2
DISCUSSION
1
61
[ "b61", "b16", "b17", "b36" ]
16,936,320
pmid-7984417|pmid-15034147|pmid-8783936|pmid-10101183|pmid-7603565|pmid-15535883
Future research should assess the strengths and weaknesses of signature genes, indels, and motifs as phylogenetic characters.
[ "61", "16", "17", "36" ]
125
8,498
0
false
Future research should assess the strengths and weaknesses of signature genes, indels, and motifs as phylogenetic characters.
[]
Future research should assess the strengths and weaknesses of signature genes, indels, and motifs as phylogenetic characters.
true
true
true
true
true
1,366
2
DISCUSSION
1
61
[ "b61", "b16", "b17", "b36" ]
16,936,320
pmid-7984417|pmid-15034147|pmid-8783936|pmid-10101183|pmid-7603565|pmid-15535883
The Listeria anomaly in Figure 3 highlights the fact that the evolutionary mechanism of insertion and deletion is not well understood.
[ "61", "16", "17", "36" ]
134
8,499
0
false
The Listeria anomaly in Figure 3 highlights the fact that the evolutionary mechanism of insertion and deletion is not well understood.
[]
The Listeria anomaly in Figure 3 highlights the fact that the evolutionary mechanism of insertion and deletion is not well understood.
true
true
true
true
true
1,366