Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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3
INTRODUCTION
1
11
[ "b11", "b17", "b18", "b20" ]
17,272,295
pmid-11489916|pmid-11864607|pmid-9548374|pmid-15629442|pmid-12110181|pmid-11071894
YFP-tagged Rrp14p was found to localize to the nucleolus (11), and we subsequently identified Rrp14p as a component of an early pre-60S complex that was co-purified with tagged Ssf1p (17), suggesting a role in ribosome synthesis.
[ "11", "17", "18", "20" ]
229
4,200
1
false
YFP-tagged Rrp14p was found to localize to the nucleolus, and we subsequently identified Rrp14p as a component of an early pre-60S complex that was co-purified with tagged Ssf1p, suggesting a role in ribosome synthesis.
[ "11", "17" ]
YFP-tagged Rrp14p was found to localize to the nucleolus, and we subsequently identified Rrp14p as a component of an early pre-60S complex that was co-purified with tagged Ssf1p, suggesting a role in ribosome synthesis.
true
true
true
true
true
715
3
INTRODUCTION
1
11
[ "b11", "b17", "b18", "b20" ]
17,272,295
pmid-11489916|pmid-11864607|pmid-9548374|pmid-15629442|pmid-12110181|pmid-11071894
Rrp14p is a member of the SURF-6 family of nucleolar proteins, which have been predicted from bioinformatic analyses to participate in complex protein–protein and protein–RNA interactions within the nucleolus (18–20).
[ "11", "17", "18", "20" ]
217
4,201
0
false
Rrp14p is a member of the SURF-6 family of nucleolar proteins, which have been predicted from bioinformatic analyses to participate in complex protein–protein and protein–RNA interactions within the nucleolus.
[ "18–20" ]
Rrp14p is a member of the SURF-6 family of nucleolar proteins, which have been predicted from bioinformatic analyses to participate in complex protein–protein and protein–RNA interactions within the nucleolus.
true
true
true
true
true
715
4
INTRODUCTION
0
null
null
17,272,295
pmid-1651172|pmid-11804586|pmid-12360190
Here we report that Rrp14p functions in ribosome synthesis; it is required for the maturation of both small and large subunit rRNAs and helps to prevent premature cleavage of the pre-rRNA at site C2.
null
199
4,202
0
false
null
null
Here we report that Rrp14p functions in ribosome synthesis; it is required for the maturation of both small and large subunit rRNAs and helps to prevent premature cleavage of the pre-rRNA at site C2.
true
true
true
true
true
716
4
INTRODUCTION
0
null
null
17,272,295
pmid-1651172|pmid-11804586|pmid-12360190
Strains depleted of Rrp14p also show defects in positioning and elongation of the mitotic spindle during mitosis, which were not previously reported for cells depleted for any other ribosome synthesis factor.
null
208
4,203
0
false
null
null
Strains depleted of Rrp14p also show defects in positioning and elongation of the mitotic spindle during mitosis, which were not previously reported for cells depleted for any other ribosome synthesis factor.
true
true
true
true
true
716
0
DISCUSSION
1
17
[ "b17", "b30" ]
17,272,295
pmid-2666845|pmid-15489289|pmid-8203157|pmid-15226434|pmid-12110181|pmid-15022016|pmid-11864607|pmid-15100437
Here we report that yeast Rrp14p functions in the synthesis of both 40S and 60S ribosomal subunits and may also play some direct role in cell-cycle progression through G2/M.
[ "17", "30" ]
173
4,204
0
false
Here we report that yeast Rrp14p functions in the synthesis of both 40S and 60S ribosomal subunits and may also play some direct role in cell-cycle progression through G2/M.
[]
Here we report that yeast Rrp14p functions in the synthesis of both 40S and 60S ribosomal subunits and may also play some direct role in cell-cycle progression through G2/M.
true
true
true
true
true
717
0
DISCUSSION
1
17
[ "b17", "b30" ]
17,272,295
pmid-2666845|pmid-15489289|pmid-8203157|pmid-15226434|pmid-12110181|pmid-15022016|pmid-11864607|pmid-15100437
Rrp14p was identified as a putative participant in 60S ribosomal subunit synthesis by its co-precipitation with early pre-60S particles that were associated with TAP-tagged Ssf1p (17) and Rrp1p (30).
[ "17", "30" ]
199
4,205
1
false
Rrp14p was identified as a putative participant in 60S ribosomal subunit synthesis by its co-precipitation with early pre-60S particles that were associated with TAP-tagged Ssf1p and Rrp1p.
[ "17", "30" ]
Rrp14p was identified as a putative participant in 60S ribosomal subunit synthesis by its co-precipitation with early pre-60S particles that were associated with TAP-tagged Ssf1p and Rrp1p.
true
true
true
true
true
717
0
DISCUSSION
1
17
[ "b17", "b30" ]
17,272,295
pmid-2666845|pmid-15489289|pmid-8203157|pmid-15226434|pmid-12110181|pmid-15022016|pmid-11864607|pmid-15100437
However, gradient analyses indicate that Rrp14p also associates with the earlier 90S pre-ribosomes, which include many of the factors required for 40S ribosome synthesis.
[ "17", "30" ]
170
4,206
0
false
However, gradient analyses indicate that Rrp14p also associates with the earlier 90S pre-ribosomes, which include many of the factors required for 40S ribosome synthesis.
[]
However, gradient analyses indicate that Rrp14p also associates with the earlier 90S pre-ribosomes, which include many of the factors required for 40S ribosome synthesis.
true
true
true
true
true
717
0
DISCUSSION
1
17
[ "b17", "b30" ]
17,272,295
pmid-2666845|pmid-15489289|pmid-8203157|pmid-15226434|pmid-12110181|pmid-15022016|pmid-11864607|pmid-15100437
In addition to inhibiting rRNA maturation, loss of Rrp14p apparently allowed premature cleavage of both the 35S and 27SA2 pre-rRNAs.
[ "17", "30" ]
132
4,207
0
false
In addition to inhibiting rRNA maturation, loss of Rrp14p apparently allowed premature cleavage of both the 35S and 27SA2 pre-rRNAs.
[]
In addition to inhibiting rRNA maturation, loss of Rrp14p apparently allowed premature cleavage of both the 35S and 27SA2 pre-rRNAs.
true
true
true
true
true
717
0
DISCUSSION
1
17
[ "b17", "b30" ]
17,272,295
pmid-2666845|pmid-15489289|pmid-8203157|pmid-15226434|pmid-12110181|pmid-15022016|pmid-11864607|pmid-15100437
We speculate that Rrp14p binds late pre-90S particles and then remains associated with the pre-60S region.
[ "17", "30" ]
106
4,208
0
false
We speculate that Rrp14p binds late pre-90S particles and then remains associated with the pre-60S region.
[]
We speculate that Rrp14p binds late pre-90S particles and then remains associated with the pre-60S region.
true
true
true
true
true
717
0
DISCUSSION
1
17
[ "b17", "b30" ]
17,272,295
pmid-2666845|pmid-15489289|pmid-8203157|pmid-15226434|pmid-12110181|pmid-15022016|pmid-11864607|pmid-15100437
As well as promoting correct maturation of both subunits, Rrp14p might act to suppress ITS1 and ITS2 cleavage until other maturation steps have occurred.
[ "17", "30" ]
153
4,209
0
false
As well as promoting correct maturation of both subunits, Rrp14p might act to suppress ITS1 and ITS2 cleavage until other maturation steps have occurred.
[]
As well as promoting correct maturation of both subunits, Rrp14p might act to suppress ITS1 and ITS2 cleavage until other maturation steps have occurred.
true
true
true
true
true
717
1
DISCUSSION
1
46
[ "b46", "b48", "b49", "b11" ]
17,272,295
pmid-15356263|pmid-12089449|NA|pmid-11489916
In addition to their unusual pre-rRNA processing defects, cells depleted of Rrp14p showed striking cell-cycle-related phenotypes.
[ "46", "48", "49", "11" ]
129
4,210
0
false
In addition to their unusual pre-rRNA processing defects, cells depleted of Rrp14p showed striking cell-cycle-related phenotypes.
[]
In addition to their unusual pre-rRNA processing defects, cells depleted of Rrp14p showed striking cell-cycle-related phenotypes.
true
true
true
true
true
718
1
DISCUSSION
1
46
[ "b46", "b48", "b49", "b11" ]
17,272,295
pmid-15356263|pmid-12089449|NA|pmid-11489916
It is difficult to exclude the possibility that these are an indirect consequence of reduced ribosomal subunit abundances.
[ "46", "48", "49", "11" ]
122
4,211
0
false
It is difficult to exclude the possibility that these are an indirect consequence of reduced ribosomal subunit abundances.
[]
It is difficult to exclude the possibility that these are an indirect consequence of reduced ribosomal subunit abundances.
true
true
true
true
true
718
1
DISCUSSION
1
46
[ "b46", "b48", "b49", "b11" ]
17,272,295
pmid-15356263|pmid-12089449|NA|pmid-11489916
However, this seems unlikely because no similar phenotypes have been reported for any of the large number of ribosome synthesis factors previously analyzed.
[ "46", "48", "49", "11" ]
156
4,212
0
false
However, this seems unlikely because no similar phenotypes have been reported for any of the large number of ribosome synthesis factors previously analyzed.
[]
However, this seems unlikely because no similar phenotypes have been reported for any of the large number of ribosome synthesis factors previously analyzed.
true
true
true
true
true
718
1
DISCUSSION
1
46
[ "b46", "b48", "b49", "b11" ]
17,272,295
pmid-15356263|pmid-12089449|NA|pmid-11489916
This phenotype is certainly not expected to result from the inhibition of translation per se, which leads to cell-cycle arrest at the ‘Start’ check point at the G1–S boundary and this is also seen in many strains with ribosome synthesis defects [(46,48) and reviewed in (49)].
[ "46", "48", "49", "11" ]
276
4,213
0
false
This phenotype is certainly not expected to result from the inhibition of translation per se, which leads to cell-cycle arrest at the ‘Start’ check point at the G1–S boundary and this is also seen in many strains with ribosome synthesis defects.
[ "(46,48) and reviewed in (49)" ]
This phenotype is certainly not expected to result from the inhibition of translation per se, which leads to cell-cycle arrest at the ‘Start’ check point at the G1–S boundary and this is also seen in many strains with ribosome synthesis defects.
true
true
true
true
true
718
1
DISCUSSION
1
11
[ "b46", "b48", "b49", "b11" ]
17,272,295
pmid-15356263|pmid-12089449|NA|pmid-11489916
Rrp14p was initially characterized in two hybrid analyses of a protein interaction network involved in the specification of cell polarity, and was predicted to be involved in polarized growth and the establishment of bud sites (11).
[ "46", "48", "49", "11" ]
232
4,214
1
false
Rrp14p was initially characterized in two hybrid analyses of a protein interaction network involved in the specification of cell polarity, and was predicted to be involved in polarized growth and the establishment of bud sites.
[ "11" ]
Rrp14p was initially characterized in two hybrid analyses of a protein interaction network involved in the specification of cell polarity, and was predicted to be involved in polarized growth and the establishment of bud sites.
true
true
true
true
true
718
1
DISCUSSION
1
46
[ "b46", "b48", "b49", "b11" ]
17,272,295
pmid-15356263|pmid-12089449|NA|pmid-11489916
Although these authors did not demonstrate the physical association of Rrp14p with proteins direct involved in cell polarity, their conclusions are at least consistent with our observations.
[ "46", "48", "49", "11" ]
190
4,215
0
false
Although these authors did not demonstrate the physical association of Rrp14p with proteins direct involved in cell polarity, their conclusions are at least consistent with our observations.
[]
Although these authors did not demonstrate the physical association of Rrp14p with proteins direct involved in cell polarity, their conclusions are at least consistent with our observations.
true
true
true
true
true
718
2
DISCUSSION
1
50
[ "b50" ]
17,272,295
pmid-11489916|pmid-10662670|pmid-7748491|pmid-14734533|pmid-9367979|pmid-11489916|pmid-15684028
Synchronized Rrp14p-depleted cells arrest with an undivided nucleus and short spindles, a phenotype characteristic of arrest at the G2/M boundary.
[ "50" ]
146
4,216
0
false
Synchronized Rrp14p-depleted cells arrest with an undivided nucleus and short spindles, a phenotype characteristic of arrest at the G2/M boundary.
[]
Synchronized Rrp14p-depleted cells arrest with an undivided nucleus and short spindles, a phenotype characteristic of arrest at the G2/M boundary.
true
true
true
true
true
719
2
DISCUSSION
1
50
[ "b50" ]
17,272,295
pmid-11489916|pmid-10662670|pmid-7748491|pmid-14734533|pmid-9367979|pmid-11489916|pmid-15684028
Moreover, the spindles are often misaligned with the bud axis, and the nuclei frequently fail to migrate to the bud neck.
[ "50" ]
121
4,217
0
false
Moreover, the spindles are often misaligned with the bud axis, and the nuclei frequently fail to migrate to the bud neck.
[]
Moreover, the spindles are often misaligned with the bud axis, and the nuclei frequently fail to migrate to the bud neck.
true
true
true
true
true
719
2
DISCUSSION
1
50
[ "b50" ]
17,272,295
pmid-11489916|pmid-10662670|pmid-7748491|pmid-14734533|pmid-9367979|pmid-11489916|pmid-15684028
In wild-type cells the nucleolus moves during mitosis from its S phase location opposite the bud neck to a position perpendicular to the bud neck (50).
[ "50" ]
151
4,218
1
false
In wild-type cells the nucleolus moves during mitosis from its S phase location opposite the bud neck to a position perpendicular to the bud neck.
[ "50" ]
In wild-type cells the nucleolus moves during mitosis from its S phase location opposite the bud neck to a position perpendicular to the bud neck.
true
true
true
true
true
719
2
DISCUSSION
1
50
[ "b50" ]
17,272,295
pmid-11489916|pmid-10662670|pmid-7748491|pmid-14734533|pmid-9367979|pmid-11489916|pmid-15684028
In most Rrp14p-depleted cells the nucleolus was incorrectly positioned, remaining located opposite the bud neck.
[ "50" ]
112
4,219
0
false
In most Rrp14p-depleted cells the nucleolus was incorrectly positioned, remaining located opposite the bud neck.
[]
In most Rrp14p-depleted cells the nucleolus was incorrectly positioned, remaining located opposite the bud neck.
true
true
true
true
true
719
2
DISCUSSION
1
50
[ "b50" ]
17,272,295
pmid-11489916|pmid-10662670|pmid-7748491|pmid-14734533|pmid-9367979|pmid-11489916|pmid-15684028
The cytoplasmic MT asters, which normally form on the cytoplasmic face of the SPBs, were also absent in Rrp14p-depleted cells.
[ "50" ]
126
4,220
0
false
The cytoplasmic MT asters, which normally form on the cytoplasmic face of the SPBs, were also absent in Rrp14p-depleted cells.
[]
The cytoplasmic MT asters, which normally form on the cytoplasmic face of the SPBs, were also absent in Rrp14p-depleted cells.
true
true
true
true
true
719
3
DISCUSSION
1
5
[ "b5", "b51" ]
17,272,295
pmid-11489916|pmid-11864607|pmid-9548374|pmid-15629442|pmid-12110181|pmid-11071894
In several mutant strains cell-cycle arrest during mitosis has been shown to be a consequence of activation of checkpoints, which respond to defects in DNA replication, spindle structure or spindle orientation.
[ "5", "51" ]
210
4,221
0
false
In several mutant strains cell-cycle arrest during mitosis has been shown to be a consequence of activation of checkpoints, which respond to defects in DNA replication, spindle structure or spindle orientation.
[]
In several mutant strains cell-cycle arrest during mitosis has been shown to be a consequence of activation of checkpoints, which respond to defects in DNA replication, spindle structure or spindle orientation.
true
true
true
true
true
720
3
DISCUSSION
1
5
[ "b5", "b51" ]
17,272,295
pmid-11489916|pmid-11864607|pmid-9548374|pmid-15629442|pmid-12110181|pmid-11071894
A mild delay in DNA replication was seen in Rrp14p-depleted cells, but this was very much less marked than the inhibition seen in cells depleted of another 60S synthesis factor, Yph1p, which associates with the DNA origin of replication complex (ORC) (5,51).
[ "5", "51" ]
258
4,222
0
false
A mild delay in DNA replication was seen in Rrp14p-depleted cells, but this was very much less marked than the inhibition seen in cells depleted of another 60S synthesis factor, Yph1p, which associates with the DNA origin of replication complex (ORC).
[ "5,51" ]
A mild delay in DNA replication was seen in Rrp14p-depleted cells, but this was very much less marked than the inhibition seen in cells depleted of another 60S synthesis factor, Yph1p, which associates with the DNA origin of replication complex (ORC).
true
true
true
true
true
720
3
DISCUSSION
1
5
[ "b5", "b51" ]
17,272,295
pmid-11489916|pmid-11864607|pmid-9548374|pmid-15629442|pmid-12110181|pmid-11071894
Moreover, 40 min after release from HU arrest, most Rrp14p-depleted cells have completed DNA replication, as judged by FACS analysis, but all are arrested at G2/M as judged by their morphology.
[ "5", "51" ]
193
4,223
0
false
Moreover, 40 min after release from HU arrest, most Rrp14p-depleted cells have completed DNA replication, as judged by FACS analysis, but all are arrested at G2/M as judged by their morphology.
[]
Moreover, 40 min after release from HU arrest, most Rrp14p-depleted cells have completed DNA replication, as judged by FACS analysis, but all are arrested at G2/M as judged by their morphology.
true
true
true
true
true
720
3
DISCUSSION
1
5
[ "b5", "b51" ]
17,272,295
pmid-11489916|pmid-11864607|pmid-9548374|pmid-15629442|pmid-12110181|pmid-11071894
It is therefore unlikely that a failure in DNA replication is responsible for the cell-cycle arrest.
[ "5", "51" ]
100
4,224
0
false
It is therefore unlikely that a failure in DNA replication is responsible for the cell-cycle arrest.
[]
It is therefore unlikely that a failure in DNA replication is responsible for the cell-cycle arrest.
true
true
true
true
true
720
4
DISCUSSION
1
52
[ "b52", "b53", "b42" ]
17,272,295
pmid-1651172|pmid-11804586|pmid-12360190
Defects in the structure of the mitotic spindle or its attachment to chromosomal centromeres are monitored by the Mad2p-dependent spindle checkpoint, while defects in spindle orientation activate a Bub2p-dependent checkpoint (52,53) [reviewed in (42)].
[ "52", "53", "42" ]
252
4,225
0
false
Defects in the structure of the mitotic spindle or its attachment to chromosomal centromeres are monitored by the Mad2p-dependent spindle checkpoint, while defects in spindle orientation activate a Bub2p-dependent checkpoint.
[ "52,53", "reviewed in (42)" ]
Defects in the structure of the mitotic spindle or its attachment to chromosomal centromeres are monitored by the Mad2p-dependent spindle checkpoint, while defects in spindle orientation activate a Bub2p-dependent checkpoint.
true
true
true
true
true
721
4
DISCUSSION
1
52
[ "b52", "b53", "b42" ]
17,272,295
pmid-1651172|pmid-11804586|pmid-12360190
To determine whether either of these checkpoints arrests Rrp14p-depleted cells, we deleted the genes encoding Mad2p and Bub2p.
[ "52", "53", "42" ]
126
4,226
0
false
To determine whether either of these checkpoints arrests Rrp14p-depleted cells, we deleted the genes encoding Mad2p and Bub2p.
[]
To determine whether either of these checkpoints arrests Rrp14p-depleted cells, we deleted the genes encoding Mad2p and Bub2p.
true
true
true
true
true
721
4
DISCUSSION
1
52
[ "b52", "b53", "b42" ]
17,272,295
pmid-1651172|pmid-11804586|pmid-12360190
The absence of Mad2p had no clear effects on the growth, DNA replication or morphology of Rrp14p-depleted cells.
[ "52", "53", "42" ]
112
4,227
0
false
The absence of Mad2p had no clear effects on the growth, DNA replication or morphology of Rrp14p-depleted cells.
[]
The absence of Mad2p had no clear effects on the growth, DNA replication or morphology of Rrp14p-depleted cells.
true
true
true
true
true
721
4
DISCUSSION
1
52
[ "b52", "b53", "b42" ]
17,272,295
pmid-1651172|pmid-11804586|pmid-12360190
In contrast, the absence of Bub2p from Rrp14p-depleted cells led to the formation of cells containing multiple SPBs, binucleate mother cells and cell chains, presumably due to ongoing bud formation and SPB duplication without cell division.
[ "52", "53", "42" ]
240
4,228
0
false
In contrast, the absence of Bub2p from Rrp14p-depleted cells led to the formation of cells containing multiple SPBs, binucleate mother cells and cell chains, presumably due to ongoing bud formation and SPB duplication without cell division.
[]
In contrast, the absence of Bub2p from Rrp14p-depleted cells led to the formation of cells containing multiple SPBs, binucleate mother cells and cell chains, presumably due to ongoing bud formation and SPB duplication without cell division.
true
true
true
true
true
721
4
DISCUSSION
1
52
[ "b52", "b53", "b42" ]
17,272,295
pmid-1651172|pmid-11804586|pmid-12360190
This observation indicates that the defect in the orientation of the spindles in Rrp14p-depleted cells is responsible for the cell-cycle arrest.
[ "52", "53", "42" ]
144
4,229
0
false
This observation indicates that the defect in the orientation of the spindles in Rrp14p-depleted cells is responsible for the cell-cycle arrest.
[]
This observation indicates that the defect in the orientation of the spindles in Rrp14p-depleted cells is responsible for the cell-cycle arrest.
true
true
true
true
true
721
5
DISCUSSION
1
54
[ "b54", "b55", "b56", "b57", "b58", "b59", "b60" ]
17,272,295
pmid-16754862|pmid-15851029|pmid-15544799|pmid-8970155|pmid-10465789|pmid-11071906|pmid-11960984
RNAs have been identified in the centrioles of surf clams (54), whereas RNA species associate with mitotic MTs in Xenopus egg extracts and spindle assembly is promoted by the RNA export factor Rae1p (55), which is structurally related to the spindle checkpoint protein Bub3p (56).
[ "54", "55", "56", "57", "58", "59", "60" ]
280
4,230
1
false
RNAs have been identified in the centrioles of surf clams, whereas RNA species associate with mitotic MTs in Xenopus egg extracts and spindle assembly is promoted by the RNA export factor Rae1p, which is structurally related to the spindle checkpoint protein Bub3p.
[ "54", "55", "56" ]
RNAs have been identified in the centrioles of surf clams, whereas RNA species associate with mitotic MTs in Xenopus egg extracts and spindle assembly is promoted by the RNA export factor Rae1p, which is structurally related to the spindle checkpoint protein Bub3p.
true
true
true
true
true
722
5
DISCUSSION
1
57
[ "b54", "b55", "b56", "b57", "b58", "b59", "b60" ]
17,272,295
pmid-16754862|pmid-15851029|pmid-15544799|pmid-8970155|pmid-10465789|pmid-11071906|pmid-11960984
Yeast Rae1p (Gle2p) (57) is implicated in the export of ribosomal subunits (58,59), but potential interactions with Rrp14p have not been directly assessed.
[ "54", "55", "56", "57", "58", "59", "60" ]
155
4,231
1
false
Yeast Rae1p (Gle2p) is implicated in the export of ribosomal subunits, but potential interactions with Rrp14p have not been directly assessed.
[ "57", "58,59" ]
Yeast Rae1p (Gle2p) is implicated in the export of ribosomal subunits, but potential interactions with Rrp14p have not been directly assessed.
true
true
true
true
true
722
5
DISCUSSION
1
60
[ "b54", "b55", "b56", "b57", "b58", "b59", "b60" ]
17,272,295
pmid-16754862|pmid-15851029|pmid-15544799|pmid-8970155|pmid-10465789|pmid-11071906|pmid-11960984
Furthermore, a proteomic analysis of 60S pre-ribosomal particles isolated from human cells identified MT-associated proteins as components of the complex (60).
[ "54", "55", "56", "57", "58", "59", "60" ]
159
4,232
1
false
Furthermore, a proteomic analysis of 60S pre-ribosomal particles isolated from human cells identified MT-associated proteins as components of the complex.
[ "60" ]
Furthermore, a proteomic analysis of 60S pre-ribosomal particles isolated from human cells identified MT-associated proteins as components of the complex.
true
true
true
true
true
722
6
DISCUSSION
0
null
null
17,272,295
null
Together these data suggest that in other systems RNA molecules associate with mitotic spindles, and it is at least conceivable that RNAs—and therefore RNA-binding proteins—also play some role in yeast spindle dynamics.
null
219
4,233
0
false
null
null
Together these data suggest that in other systems RNA molecules associate with mitotic spindles, and it is at least conceivable that RNAs—and therefore RNA-binding proteins—also play some role in yeast spindle dynamics.
true
true
true
true
true
723
0
INTRODUCTION
1
1
[ "b1", "b2", "b6" ]
17,135,211
pmid-12200227|pmid-12824413|pmid-15448370
Polymerase chain reaction (PCR) is a widely accepted method for clinical detection of pathogens due to its speed, sensitivity and specificity (1).
[ "1", "2", "6" ]
146
4,234
1
false
Polymerase chain reaction (PCR) is a widely accepted method for clinical detection of pathogens due to its speed, sensitivity and specificity.
[ "1" ]
Polymerase chain reaction (PCR) is a widely accepted method for clinical detection of pathogens due to its speed, sensitivity and specificity.
true
true
true
true
true
724
0
INTRODUCTION
1
1
[ "b1", "b2", "b6" ]
17,135,211
pmid-12200227|pmid-12824413|pmid-15448370
PCR detection of viruses, especially RNA and retroviruses, is complicated by their high mutation rates.
[ "1", "2", "6" ]
103
4,235
0
false
PCR detection of viruses, especially RNA and retroviruses, is complicated by their high mutation rates.
[]
PCR detection of viruses, especially RNA and retroviruses, is complicated by their high mutation rates.
true
true
true
true
true
724
0
INTRODUCTION
1
1
[ "b1", "b2", "b6" ]
17,135,211
pmid-12200227|pmid-12824413|pmid-15448370
Thus, primers for virus detection are frequently designed to amplify highly conserved regions, where binding sites are most likely to be retained.
[ "1", "2", "6" ]
146
4,236
0
false
Thus, primers for virus detection are frequently designed to amplify highly conserved regions, where binding sites are most likely to be retained.
[]
Thus, primers for virus detection are frequently designed to amplify highly conserved regions, where binding sites are most likely to be retained.
true
true
true
true
true
724
0
INTRODUCTION
1
1
[ "b1", "b2", "b6" ]
17,135,211
pmid-12200227|pmid-12824413|pmid-15448370
By synthesizing primers with degenerate positions, all the possible variants of a target sequence can be covered.
[ "1", "2", "6" ]
113
4,237
0
false
By synthesizing primers with degenerate positions, all the possible variants of a target sequence can be covered.
[]
By synthesizing primers with degenerate positions, all the possible variants of a target sequence can be covered.
true
true
true
true
true
724
0
INTRODUCTION
1
1
[ "b1", "b2", "b6" ]
17,135,211
pmid-12200227|pmid-12824413|pmid-15448370
This method has been successfully applied to both pathogen detection and cloning of homologous genes (2–6).
[ "1", "2", "6" ]
107
4,238
0
false
This method has been successfully applied to both pathogen detection and cloning of homologous genes.
[ "2–6" ]
This method has been successfully applied to both pathogen detection and cloning of homologous genes.
true
true
true
true
true
724
1
INTRODUCTION
0
null
null
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
Although the use of degenerate primers increases the flexibility of PCR applications it also increases the complexity of primer design.
null
135
4,239
0
false
null
null
Although the use of degenerate primers increases the flexibility of PCR applications it also increases the complexity of primer design.
true
true
true
true
true
725
1
INTRODUCTION
0
null
null
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
Degeneracy is a critical factor in the sensitivity of PCR because a highly degenerate primer will have few species that precisely match the template.
null
149
4,240
0
false
null
null
Degeneracy is a critical factor in the sensitivity of PCR because a highly degenerate primer will have few species that precisely match the template.
true
true
true
true
true
725
1
INTRODUCTION
0
null
null
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
In early rounds of PCR, the more homologous primers will likely be incorporated into products.
null
94
4,241
0
false
null
null
In early rounds of PCR, the more homologous primers will likely be incorporated into products.
true
true
true
true
true
725
1
INTRODUCTION
0
null
null
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
The efficiency with which amplification proceeds in subsequent cycles is dependent on the similarity of the remaining primers in the pool.
null
138
4,242
0
false
null
null
The efficiency with which amplification proceeds in subsequent cycles is dependent on the similarity of the remaining primers in the pool.
true
true
true
true
true
725
1
INTRODUCTION
0
null
null
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
Hence, primers with the least number of degenerate positions have the greatest likelihood of success.
null
101
4,243
0
false
null
null
Hence, primers with the least number of degenerate positions have the greatest likelihood of success.
true
true
true
true
true
725
1
INTRODUCTION
0
null
null
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
The objective of degenerate primer design is to balance the coverage of variant sequences with the negative implications of degeneracy.
null
135
4,244
0
false
null
null
The objective of degenerate primer design is to balance the coverage of variant sequences with the negative implications of degeneracy.
true
true
true
true
true
725
2
INTRODUCTION
1
7
[ "b7", "b8", "b12", "b13", "b14", "b15", "b11", "b2", "b13", "b12", "b16", "b17", "b18", "b19" ]
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
A consensus has emerged regarding appropriate GC content, acceptable hairpin lengths, melting temperature and maximum homopolymeric runs for primers (7).
[ "7", "8", "12", "13", "14", "15", "11", "2", "13", "12", "16", "17", "18", "19" ]
153
4,245
1
false
A consensus has emerged regarding appropriate GC content, acceptable hairpin lengths, melting temperature and maximum homopolymeric runs for primers.
[ "7" ]
A consensus has emerged regarding appropriate GC content, acceptable hairpin lengths, melting temperature and maximum homopolymeric runs for primers.
true
true
true
true
true
726
2
INTRODUCTION
1
7
[ "b7", "b8", "b12", "b13", "b14", "b15", "b11", "b2", "b13", "b12", "b16", "b17", "b18", "b19" ]
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
Based on these considerations, many software tools have been written for the design of non-degenerate primers (8–12).
[ "7", "8", "12", "13", "14", "15", "11", "2", "13", "12", "16", "17", "18", "19" ]
117
4,246
0
false
Based on these considerations, many software tools have been written for the design of non-degenerate primers.
[ "8–12" ]
Based on these considerations, many software tools have been written for the design of non-degenerate primers.
true
true
true
true
true
726
2
INTRODUCTION
1
13
[ "b7", "b8", "b12", "b13", "b14", "b15", "b11", "b2", "b13", "b12", "b16", "b17", "b18", "b19" ]
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
Degenerate and multiplex primer design has been classified as an optimization problem (13).
[ "7", "8", "12", "13", "14", "15", "11", "2", "13", "12", "16", "17", "18", "19" ]
91
4,247
1
false
Degenerate and multiplex primer design has been classified as an optimization problem.
[ "13" ]
Degenerate and multiplex primer design has been classified as an optimization problem.
true
true
true
true
true
726
2
INTRODUCTION
1
7
[ "b7", "b8", "b12", "b13", "b14", "b15", "b11", "b2", "b13", "b12", "b16", "b17", "b18", "b19" ]
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
Thus, heuristic algorithms have been particularly useful in addressing the challenge.
[ "7", "8", "12", "13", "14", "15", "11", "2", "13", "12", "16", "17", "18", "19" ]
85
4,248
0
false
Thus, heuristic algorithms have been particularly useful in addressing the challenge.
[]
Thus, heuristic algorithms have been particularly useful in addressing the challenge.
true
true
true
true
true
726
2
INTRODUCTION
1
12
[ "b7", "b8", "b12", "b13", "b14", "b15", "b11", "b2", "b13", "b12", "b16", "b17", "b18", "b19" ]
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
Examples include the methods of Doi and Imai (14), GeneFisher (15), PRIMEGENS (11), CODEHOP (2), HYDEN (13), PROBEmer (12), MIPS (16), Amplicon (17), PDA-MS/UniQ (18) and MuPlex (19).
[ "7", "8", "12", "13", "14", "15", "11", "2", "13", "12", "16", "17", "18", "19" ]
183
4,249
1
false
Examples include the methods of Doi and Imai, GeneFisher, PRIMEGENS, CODEHOP, HYDEN, PROBEmer, MIPS, Amplicon, PDA-MS/UniQ and MuPlex.
[ "14", "15", "11", "2", "13", "12", "16", "17", "18", "19" ]
Examples include the methods of Doi and Imai, GeneFisher, PRIMEGENS, CODEHOP, HYDEN, PROBEmer, MIPS, Amplicon, PDA-MS/UniQ and MuPlex.
true
true
true
true
true
726
3
INTRODUCTION
1
20
[ "b20", "b21", "b23", "b24", "b25", "b26", "b27", "b18", "b28", "b29" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
More sophisticated algorithms for primer design, coupled to intuitive public interfaces are becoming necessary to address the increase of sequence information in microbiology.
[ "20", "21", "23", "24", "25", "26", "27", "18", "28", "29" ]
175
4,250
0
false
More sophisticated algorithms for primer design, coupled to intuitive public interfaces are becoming necessary to address the increase of sequence information in microbiology.
[]
More sophisticated algorithms for primer design, coupled to intuitive public interfaces are becoming necessary to address the increase of sequence information in microbiology.
true
true
true
true
true
727
3
INTRODUCTION
1
20
[ "b20", "b21", "b23", "b24", "b25", "b26", "b27", "b18", "b28", "b29" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
Our work builds on the idea that primer design is an optimization problem that can be solved by adapting methods from computer science.
[ "20", "21", "23", "24", "25", "26", "27", "18", "28", "29" ]
135
4,251
0
false
Our work builds on the idea that primer design is an optimization problem that can be solved by adapting methods from computer science.
[]
Our work builds on the idea that primer design is an optimization problem that can be solved by adapting methods from computer science.
true
true
true
true
true
727
3
INTRODUCTION
1
20
[ "b20", "b21", "b23", "b24", "b25", "b26", "b27", "b18", "b28", "b29" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
The Set Covering Problem (SCP) has classically been used to describe an airline crew scheduling problem, wherein a group of crews must travel to a set of destinations with minimal cost.
[ "20", "21", "23", "24", "25", "26", "27", "18", "28", "29" ]
185
4,252
0
false
The Set Covering Problem (SCP) has classically been used to describe an airline crew scheduling problem, wherein a group of crews must travel to a set of destinations with minimal cost.
[]
The Set Covering Problem (SCP) has classically been used to describe an airline crew scheduling problem, wherein a group of crews must travel to a set of destinations with minimal cost.
true
true
true
true
true
727
3
INTRODUCTION
1
20
[ "b20", "b21", "b23", "b24", "b25", "b26", "b27", "b18", "b28", "b29" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
A brute force solution, which is an evaluation of all combinations of ‘schedules’, becomes computational intractable with only a few thousand possibilities.
[ "20", "21", "23", "24", "25", "26", "27", "18", "28", "29" ]
156
4,253
0
false
A brute force solution, which is an evaluation of all combinations of ‘schedules’, becomes computational intractable with only a few thousand possibilities.
[]
A brute force solution, which is an evaluation of all combinations of ‘schedules’, becomes computational intractable with only a few thousand possibilities.
true
true
true
true
true
727
3
INTRODUCTION
1
20
[ "b20", "b21", "b23", "b24", "b25", "b26", "b27", "b18", "b28", "b29" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
The SCP has been classified as NP Complete (20), meaning that no deterministic algorithm can solve it in polynomial time.
[ "20", "21", "23", "24", "25", "26", "27", "18", "28", "29" ]
121
4,254
1
false
The SCP has been classified as NP Complete, meaning that no deterministic algorithm can solve it in polynomial time.
[ "20" ]
The SCP has been classified as NP Complete, meaning that no deterministic algorithm can solve it in polynomial time.
true
true
true
true
true
727
3
INTRODUCTION
1
24
[ "b20", "b21", "b23", "b24", "b25", "b26", "b27", "b18", "b28", "b29" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
A variety of approximation algorithms exist for solving the SCP (21–23); the most straightforward is a classical greedy method (24)
[ "20", "21", "23", "24", "25", "26", "27", "18", "28", "29" ]
131
4,255
1
false
A variety of approximation algorithms exist for solving the SCP ; the most straightforward is a classical greedy method
[ "21–23", "24" ]
A variety of approximation algorithms exist for solving the SCP ; the most straightforward is a classical greedy method
true
true
false
true
false
727
3
INTRODUCTION
1
20
[ "b20", "b21", "b23", "b24", "b25", "b26", "b27", "b18", "b28", "b29" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
[for a review, see Caprara et al.
[ "20", "21", "23", "24", "25", "26", "27", "18", "28", "29" ]
33
4,256
0
false
[for a review, see Caprara et al.
[]
[for a review, see Caprara et al.
false
false
true
true
false
727
3
INTRODUCTION
1
26
[ "b20", "b21", "b23", "b24", "b25", "b26", "b27", "b18", "b28", "b29" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
SCP solving algorithms have been applied in HLA typing (26), identifying RNAi sequences (27), primer minimization in Multiplex PCR (18,28) and recently for creating oligonucleotide microarrays (29).
[ "20", "21", "23", "24", "25", "26", "27", "18", "28", "29" ]
198
4,257
1
false
SCP solving algorithms have been applied in HLA typing, identifying RNAi sequences, primer minimization in Multiplex PCR and recently for creating oligonucleotide microarrays.
[ "26", "27", "18,28", "29" ]
SCP solving algorithms have been applied in HLA typing, identifying RNAi sequences, primer minimization in Multiplex PCR and recently for creating oligonucleotide microarrays.
true
true
true
true
true
727
4
INTRODUCTION
0
null
null
17,135,211
null
In this report we describe SCPrimer, a program that determines optimum primer pairs from multiple nucleic acid sequence alignments.
null
131
4,258
0
false
null
null
In this report we describe SCPrimer, a program that determines optimum primer pairs from multiple nucleic acid sequence alignments.
true
true
true
true
true
728
4
INTRODUCTION
0
null
null
17,135,211
null
The program first computes phylogenetic trees to identify candidate primers, and then uses a greedy SCP solving algorithm to identify the minimum set that will amplify all members of the alignment.
null
197
4,259
0
false
null
null
The program first computes phylogenetic trees to identify candidate primers, and then uses a greedy SCP solving algorithm to identify the minimum set that will amplify all members of the alignment.
true
true
true
true
true
728
0
DISCUSSION
0
null
null
17,135,211
pmid-12200227|pmid-12824413|pmid-15448370
The objective of SCPrimer is to provide a simple program for standardized consensus primer design that facilitates the development of multiplex assays and extracts the minimum primer set required to address complex alignments.
null
226
4,260
0
false
null
null
The objective of SCPrimer is to provide a simple program for standardized consensus primer design that facilitates the development of multiplex assays and extracts the minimum primer set required to address complex alignments.
true
true
true
true
true
729
1
DISCUSSION
1
37
[ "b37", "b38", "b39", "b40", "b41" ]
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
VHFs are triggered by an infection with filoviruses (Ebola Virus or Marburg virus), arenaviruses (Junin, Machupo or Lassa viruses), bunyaviruses (Congo-Crimean hemorrhagic fever or Rift Valley fever) or flaviviruses (Omsk hemorrhagic fever, Kyasanur Forest disease virus or Yellow Fever virus) (37,38).
[ "37", "38", "39", "40", "41" ]
302
4,261
0
false
VHFs are triggered by an infection with filoviruses (Ebola Virus or Marburg virus), arenaviruses (Junin, Machupo or Lassa viruses), bunyaviruses (Congo-Crimean hemorrhagic fever or Rift Valley fever) or flaviviruses (Omsk hemorrhagic fever, Kyasanur Forest disease virus or Yellow Fever virus).
[ "37,38" ]
VHFs are triggered by an infection with filoviruses (Ebola Virus or Marburg virus), arenaviruses (Junin, Machupo or Lassa viruses), bunyaviruses (Congo-Crimean hemorrhagic fever or Rift Valley fever) or flaviviruses (Omsk hemorrhagic fever, Kyasanur Forest disease virus or Yellow Fever virus).
true
true
true
true
true
730
1
DISCUSSION
1
37
[ "b37", "b38", "b39", "b40", "b41" ]
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
VHF agents pose a significant problem for public health because of high morbidity, mortality and the potential for rapid spread.
[ "37", "38", "39", "40", "41" ]
128
4,262
0
false
VHF agents pose a significant problem for public health because of high morbidity, mortality and the potential for rapid spread.
[]
VHF agents pose a significant problem for public health because of high morbidity, mortality and the potential for rapid spread.
true
true
true
true
true
730
1
DISCUSSION
1
39
[ "b37", "b38", "b39", "b40", "b41" ]
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
Their evolution poses a continuous challenge to the utility of diagnostic PCR assays (39).
[ "37", "38", "39", "40", "41" ]
90
4,263
1
false
Their evolution poses a continuous challenge to the utility of diagnostic PCR assays.
[ "39" ]
Their evolution poses a continuous challenge to the utility of diagnostic PCR assays.
true
true
true
true
true
730
1
DISCUSSION
1
37
[ "b37", "b38", "b39", "b40", "b41" ]
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
SCPrimer enables the continuous update of diagnostic panels and is well suited to outbreak applications, as the reported VHF primers were designed in hours.
[ "37", "38", "39", "40", "41" ]
156
4,264
0
false
SCPrimer enables the continuous update of diagnostic panels and is well suited to outbreak applications, as the reported VHF primers were designed in hours.
[]
SCPrimer enables the continuous update of diagnostic panels and is well suited to outbreak applications, as the reported VHF primers were designed in hours.
true
true
true
true
true
730
1
DISCUSSION
1
37
[ "b37", "b38", "b39", "b40", "b41" ]
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
By matching critical parameters like the Tm, 3′ clamp length and number of degenerate positions, primers designed for different viruses behave uniformly in PCR.
[ "37", "38", "39", "40", "41" ]
160
4,265
0
false
By matching critical parameters like the Tm, 3′ clamp length and number of degenerate positions, primers designed for different viruses behave uniformly in PCR.
[]
By matching critical parameters like the Tm, 3′ clamp length and number of degenerate positions, primers designed for different viruses behave uniformly in PCR.
true
true
true
true
true
730
1
DISCUSSION
1
37
[ "b37", "b38", "b39", "b40", "b41" ]
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
Prediction of cross reactivity among primer sets is a feature which will be incorporated into later versions of SCPrimer.
[ "37", "38", "39", "40", "41" ]
121
4,266
0
false
Prediction of cross reactivity among primer sets is a feature which will be incorporated into later versions of SCPrimer.
[]
Prediction of cross reactivity among primer sets is a feature which will be incorporated into later versions of SCPrimer.
true
true
true
true
true
730
1
DISCUSSION
1
40
[ "b37", "b38", "b39", "b40", "b41" ]
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
A different multiplex VHF primer panel, created with a beta-version of the program, was successfully applied in MassTag PCR detection of VHF agents in clinical specimens (40).
[ "37", "38", "39", "40", "41" ]
175
4,267
1
false
A different multiplex VHF primer panel, created with a beta-version of the program, was successfully applied in MassTag PCR detection of VHF agents in clinical specimens.
[ "40" ]
A different multiplex VHF primer panel, created with a beta-version of the program, was successfully applied in MassTag PCR detection of VHF agents in clinical specimens.
true
true
true
true
true
730
1
DISCUSSION
1
41
[ "b37", "b38", "b39", "b40", "b41" ]
17,135,211
pmid-12404808|pmid-15577929|pmid-12615304|pmid-16704825|pmid-15752453
MassTag PCR is a diagnostic platform wherein primers labeled with photo-labile unique mass signatures are used to identify the presence of genetic targets (41).
[ "37", "38", "39", "40", "41" ]
160
4,268
1
false
MassTag PCR is a diagnostic platform wherein primers labeled with photo-labile unique mass signatures are used to identify the presence of genetic targets.
[ "41" ]
MassTag PCR is a diagnostic platform wherein primers labeled with photo-labile unique mass signatures are used to identify the presence of genetic targets.
true
true
true
true
true
730
2
DISCUSSION
0
null
null
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
Influenza viruses have emerged as high-priority pathogens with global dissemination of H5N1 and appreciation of its pandemic potential.
null
135
4,269
0
false
null
null
Influenza viruses have emerged as high-priority pathogens with global dissemination of H5N1 and appreciation of its pandemic potential.
true
true
true
true
true
731
2
DISCUSSION
0
null
null
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
More than 4000 H5N1 sequences were deposited in GenBank through May 2006; thus, the design of HA5 consensus primers is a daunting task using a multiple alignment strategy.
null
171
4,270
0
false
null
null
More than 4000 H5N1 sequences were deposited in GenBank through May 2006; thus, the design of HA5 consensus primers is a daunting task using a multiple alignment strategy.
true
true
true
true
true
731
2
DISCUSSION
0
null
null
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
If the HA5 forward primer was designed using a standard consensus method, it would comprise 3072 species to cover all sequences without mismatches.
null
147
4,271
0
false
null
null
If the HA5 forward primer was designed using a standard consensus method, it would comprise 3072 species to cover all sequences without mismatches.
true
true
true
true
true
731
2
DISCUSSION
0
null
null
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
This is not practical.
null
22
4,272
0
false
null
null
This is not practical.
true
true
true
true
true
731
2
DISCUSSION
0
null
null
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
One approach to the problem of reducing degeneracy in primer design is to split the alignment by genotype and then identify consensus sequences for each subgroup alignment.
null
172
4,273
0
false
null
null
One approach to the problem of reducing degeneracy in primer design is to split the alignment by genotype and then identify consensus sequences for each subgroup alignment.
true
true
true
true
true
731
2
DISCUSSION
0
null
null
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
This strategy is time consuming; many combinations would be identified and each potential solution would have to be evaluated independently.
null
140
4,274
0
false
null
null
This strategy is time consuming; many combinations would be identified and each potential solution would have to be evaluated independently.
true
true
true
true
true
731
2
DISCUSSION
0
null
null
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
The tree building and greedy heuristic employed in SCPrimer is a natural solution to such combinatorial problems.
null
113
4,275
0
false
null
null
The tree building and greedy heuristic employed in SCPrimer is a natural solution to such combinatorial problems.
true
true
true
true
true
731
2
DISCUSSION
0
null
null
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
For example, SCPrimer identified a minimum set of four forward primers for the HA5 alignment that would address all known targets.
null
130
4,276
0
false
null
null
For example, SCPrimer identified a minimum set of four forward primers for the HA5 alignment that would address all known targets.
true
true
true
true
true
731
2
DISCUSSION
0
null
null
17,135,211
pmid-10489613|NA|pmid-12824409|pmid-12169545|NA|pmid-8877506|pmid-12424113|pmid-12824413|pmid-12169545|pmid-12824409|NA|pmid-14962918|pmid-16249263|pmid-15980531
A single degenerate primer covered 96.3% of sequences; three additional primers were needed to cover the remaining sequences.
null
125
4,277
0
false
null
null
A single degenerate primer covered 96.3% of sequences; three additional primers were needed to cover the remaining sequences.
true
true
true
true
true
731
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
CODEHOP has been used to identify new DNA viruses (42), and is therefore of particular interest for microbiologists working in pathogen discovery.
[ "42" ]
146
4,278
1
false
CODEHOP has been used to identify new DNA viruses, and is therefore of particular interest for microbiologists working in pathogen discovery.
[ "42" ]
CODEHOP has been used to identify new DNA viruses, and is therefore of particular interest for microbiologists working in pathogen discovery.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
CODEHOP is a program for degenerate primer design that is most similar to SCPrimer.
[ "42" ]
83
4,279
0
false
CODEHOP is a program for degenerate primer design that is most similar to SCPrimer.
[]
CODEHOP is a program for degenerate primer design that is most similar to SCPrimer.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
However, the emphasis of CODEHOP is different from that of SCPrimer; CODEHOP performs exclusively at the amino acid level and tries to identify all theoretically possible nucleic acid coding variants resulting from the degenerate genetic code.
[ "42" ]
243
4,280
0
false
However, the emphasis of CODEHOP is different from that of SCPrimer; CODEHOP performs exclusively at the amino acid level and tries to identify all theoretically possible nucleic acid coding variants resulting from the degenerate genetic code.
[]
However, the emphasis of CODEHOP is different from that of SCPrimer; CODEHOP performs exclusively at the amino acid level and tries to identify all theoretically possible nucleic acid coding variants resulting from the degenerate genetic code.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
Thereby it does not, and does not attempt to, minimize the degeneracy of the primer.
[ "42" ]
84
4,281
0
false
Thereby it does not, and does not attempt to, minimize the degeneracy of the primer.
[]
Thereby it does not, and does not attempt to, minimize the degeneracy of the primer.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
SCPrimer restricts its scope to all variants represented in an alignment and attempts to provide the best solution for a user-defined maximum degeneracy per primer.
[ "42" ]
164
4,282
0
false
SCPrimer restricts its scope to all variants represented in an alignment and attempts to provide the best solution for a user-defined maximum degeneracy per primer.
[]
SCPrimer restricts its scope to all variants represented in an alignment and attempts to provide the best solution for a user-defined maximum degeneracy per primer.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
In addition, the input for the web-based version of CODEHOP requires ungapped amino acid alignments of maximum width 55.
[ "42" ]
120
4,283
0
false
In addition, the input for the web-based version of CODEHOP requires ungapped amino acid alignments of maximum width 55.
[]
In addition, the input for the web-based version of CODEHOP requires ungapped amino acid alignments of maximum width 55.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
Thus, it cannot address the comprehensive influenza HA5 alignment of width 600.
[ "42" ]
79
4,284
0
false
Thus, it cannot address the comprehensive influenza HA5 alignment of width 600.
[]
Thus, it cannot address the comprehensive influenza HA5 alignment of width 600.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
We compared primers designed by CODEHOP for a 55 amino acid region which encompassed the HA5 primer-binding sites identified by SCPrimer.
[ "42" ]
137
4,285
0
false
We compared primers designed by CODEHOP for a 55 amino acid region which encompassed the HA5 primer-binding sites identified by SCPrimer.
[]
We compared primers designed by CODEHOP for a 55 amino acid region which encompassed the HA5 primer-binding sites identified by SCPrimer.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
We executed CODEHOP with default settings and selected the least degenerate primer pair with a Tm near 60°C for analysis.
[ "42" ]
121
4,286
0
false
We executed CODEHOP with default settings and selected the least degenerate primer pair with a Tm near 60°C for analysis.
[]
We executed CODEHOP with default settings and selected the least degenerate primer pair with a Tm near 60°C for analysis.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
The CODEHOP forward primer (CGTGACCCACGCCcarrayathyt) overlapped the 3′ end of the HA5F primer-binding site and had a degeneracy of 48.
[ "42" ]
135
4,287
0
false
The CODEHOP forward primer (CGTGACCCACGCCcarrayathyt) overlapped the 3′ end of the HA5F primer-binding site and had a degeneracy of 48.
[]
The CODEHOP forward primer (CGTGACCCACGCCcarrayathyt) overlapped the 3′ end of the HA5F primer-binding site and had a degeneracy of 48.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
Upon comparison with the nucleic acid alignment, the primer had between three and five mismatches to every sequence.
[ "42" ]
116
4,288
0
false
Upon comparison with the nucleic acid alignment, the primer had between three and five mismatches to every sequence.
[]
Upon comparison with the nucleic acid alignment, the primer had between three and five mismatches to every sequence.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
The reverse primer (ggntacacrctGCTCAAGTAGTTGCACGG) had degeneracy of eight, and between one and six mismatches to all sequences.
[ "42" ]
128
4,289
0
false
The reverse primer (ggntacacrctGCTCAAGTAGTTGCACGG) had degeneracy of eight, and between one and six mismatches to all sequences.
[]
The reverse primer (ggntacacrctGCTCAAGTAGTTGCACGG) had degeneracy of eight, and between one and six mismatches to all sequences.
true
true
true
true
true
732
3
DISCUSSION
1
42
[ "b42" ]
17,135,211
NA|NA|NA|NA|NA|pmid-86406|pmid-16084706|pmid-16249263|NA|NA|pmid-15769292
Given that sensitivity decreases with increasing complexity of primer panels, the primers designed by CODEHOP may be sufficient for identifying known and novel sequences where transcripts are abundant, but may perform inefficiently in diagnostic PCR where sensitivity is critical.
[ "42" ]
280
4,290
0
false
Given that sensitivity decreases with increasing complexity of primer panels, the primers designed by CODEHOP may be sufficient for identifying known and novel sequences where transcripts are abundant, but may perform inefficiently in diagnostic PCR where sensitivity is critical.
[]
Given that sensitivity decreases with increasing complexity of primer panels, the primers designed by CODEHOP may be sufficient for identifying known and novel sequences where transcripts are abundant, but may perform inefficiently in diagnostic PCR where sensitivity is critical.
true
true
true
true
true
732
4
DISCUSSION
0
null
null
17,135,211
null
SCPrimer was created to address the specific needs of virologists and bacteriologists in creating primers for pathogen detection.
null
129
4,291
0
false
null
null
SCPrimer was created to address the specific needs of virologists and bacteriologists in creating primers for pathogen detection.
true
true
true
true
true
733
4
DISCUSSION
0
null
null
17,135,211
null
Although an ‘optimum’ sequence could be estimated by a more complicated scoring mechanism, this would not reflect the reality of experimental PCR.
null
146
4,292
0
false
null
null
Although an ‘optimum’ sequence could be estimated by a more complicated scoring mechanism, this would not reflect the reality of experimental PCR.
true
true
true
true
true
733
4
DISCUSSION
0
null
null
17,135,211
null
Investigators who wish to generate assays with highest sensitivity generally tune several potential primer pairs.
null
113
4,293
0
false
null
null
Investigators who wish to generate assays with highest sensitivity generally tune several potential primer pairs.
true
true
true
true
true
733
4
DISCUSSION
0
null
null
17,135,211
null
Owing to the investment required to develop, optimize and validate diagnostic primers, an automated design program provides a reliable starting point for experimental evaluation.
null
178
4,294
0
false
null
null
Owing to the investment required to develop, optimize and validate diagnostic primers, an automated design program provides a reliable starting point for experimental evaluation.
true
true
true
true
true
733
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8" ]
17,439,965
pmid-15372042|pmid-17011485|pmid-16814728|pmid-16557279|pmid-16141076|pmid-16736018|pmid-16258535|pmid-16459310
MiRNAs are an abundant class of non-coding RNA ranging from 20 to 23 nt of length that are post-transcriptional regulators of gene expression.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
142
4,295
0
false
MiRNAs are an abundant class of non-coding RNA ranging from 20 to 23 nt of length that are post-transcriptional regulators of gene expression.
[]
MiRNAs are an abundant class of non-coding RNA ranging from 20 to 23 nt of length that are post-transcriptional regulators of gene expression.
true
true
true
true
true
734
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8" ]
17,439,965
pmid-15372042|pmid-17011485|pmid-16814728|pmid-16557279|pmid-16141076|pmid-16736018|pmid-16258535|pmid-16459310
MiRNAs have been mainly associated with developmental processes in metazoa such as Caenorhabditis elegans or Drosophila melanogaster (1).
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
137
4,296
1
false
MiRNAs have been mainly associated with developmental processes in metazoa such as Caenorhabditis elegans or Drosophila melanogaster.
[ "1" ]
MiRNAs have been mainly associated with developmental processes in metazoa such as Caenorhabditis elegans or Drosophila melanogaster.
true
true
true
true
true
734
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8" ]
17,439,965
pmid-15372042|pmid-17011485|pmid-16814728|pmid-16557279|pmid-16141076|pmid-16736018|pmid-16258535|pmid-16459310
However, evidence also suggests a role for miRNAs in a wide range of functions in mammals, including insulin secretion, heart, skeletal muscle and brain development (2,3).
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
171
4,297
0
false
However, evidence also suggests a role for miRNAs in a wide range of functions in mammals, including insulin secretion, heart, skeletal muscle and brain development.
[ "2,3" ]
However, evidence also suggests a role for miRNAs in a wide range of functions in mammals, including insulin secretion, heart, skeletal muscle and brain development.
true
true
true
true
true
734
0
INTRODUCTION
1
4
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8" ]
17,439,965
pmid-15372042|pmid-17011485|pmid-16814728|pmid-16557279|pmid-16141076|pmid-16736018|pmid-16258535|pmid-16459310
Furthermore, miRNAs have been implicated in diseases such as cancer (4) and hepatitis C (5), which make them attractive new drug targets.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
137
4,298
1
false
Furthermore, miRNAs have been implicated in diseases such as cancer and hepatitis C, which make them attractive new drug targets.
[ "4", "5" ]
Furthermore, miRNAs have been implicated in diseases such as cancer and hepatitis C, which make them attractive new drug targets.
true
true
true
true
true
734
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8" ]
17,439,965
pmid-15372042|pmid-17011485|pmid-16814728|pmid-16557279|pmid-16141076|pmid-16736018|pmid-16258535|pmid-16459310
In contrast to the widely used RNAi technology using small interfering RNA (siRNA) duplexes, strategies to inhibit miRNAs have been less well investigated.
[ "1", "2", "3", "4", "5", "6", "7", "8" ]
155
4,299
0
false
In contrast to the widely used RNAi technology using small interfering RNA (siRNA) duplexes, strategies to inhibit miRNAs have been less well investigated.
[]
In contrast to the widely used RNAi technology using small interfering RNA (siRNA) duplexes, strategies to inhibit miRNAs have been less well investigated.
true
true
true
true
true
734