Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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1
INTRODUCTION
1
11
[ "B11", "B12", "B13", "B14", "B15", "B16 B17 B18" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
Although RT-PCR is a highly sensitive and convenient technique to analyze quantitative aspects of RNA molecules, qualitative information, such as the type or position of modified nucleosides in an RNA molecule, is not readily available through PCR.
[ "11", "12", "13", "14", "15", "16–18" ]
248
6,500
0
false
Although RT-PCR is a highly sensitive and convenient technique to analyze quantitative aspects of RNA molecules, qualitative information, such as the type or position of modified nucleosides in an RNA molecule, is not readily available through PCR.
[]
Although RT-PCR is a highly sensitive and convenient technique to analyze quantitative aspects of RNA molecules, qualitative information, such as the type or position of modified nucleosides in an RNA molecule, is not readily available through PCR.
true
true
true
true
true
1,071
1
INTRODUCTION
1
11
[ "B11", "B12", "B13", "B14", "B15", "B16 B17 B18" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
To obtain information on the functional aspects of R2NA molecules, it is desirable to employ fully processed natural RNA molecules obtained from the cell.
[ "11", "12", "13", "14", "15", "16–18" ]
154
6,501
0
false
To obtain information on the functional aspects of R2NA molecules, it is desirable to employ fully processed natural RNA molecules obtained from the cell.
[]
To obtain information on the functional aspects of R2NA molecules, it is desirable to employ fully processed natural RNA molecules obtained from the cell.
true
true
true
true
true
1,071
1
INTRODUCTION
1
11
[ "B11", "B12", "B13", "B14", "B15", "B16 B17 B18" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
Isolation of individual RNA species, however, has required complex and technically challenging procedures, which are both time-consuming and labor intensive.
[ "11", "12", "13", "14", "15", "16–18" ]
157
6,502
0
false
Isolation of individual RNA species, however, has required complex and technically challenging procedures, which are both time-consuming and labor intensive.
[]
Isolation of individual RNA species, however, has required complex and technically challenging procedures, which are both time-consuming and labor intensive.
true
true
true
true
true
1,071
1
INTRODUCTION
1
11
[ "B11", "B12", "B13", "B14", "B15", "B16 B17 B18" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
In fact, most RNA research has no choice other than to ignore the precise characterization of RNA modifications.
[ "11", "12", "13", "14", "15", "16–18" ]
112
6,503
0
false
In fact, most RNA research has no choice other than to ignore the precise characterization of RNA modifications.
[]
In fact, most RNA research has no choice other than to ignore the precise characterization of RNA modifications.
true
true
true
true
true
1,071
1
INTRODUCTION
1
11
[ "B11", "B12", "B13", "B14", "B15", "B16 B17 B18" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
Thus, development of highly efficient and convenient methods for isolation of individual RNA species will provide a fundamental strategy to enable characterization of the functional aspects of large numbers of RNA molecules.
[ "11", "12", "13", "14", "15", "16–18" ]
224
6,504
0
false
Thus, development of highly efficient and convenient methods for isolation of individual RNA species will provide a fundamental strategy to enable characterization of the functional aspects of large numbers of RNA molecules.
[]
Thus, development of highly efficient and convenient methods for isolation of individual RNA species will provide a fundamental strategy to enable characterization of the functional aspects of large numbers of RNA molecules.
true
true
true
true
true
1,071
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
For efficient isolation of individual RNAs, we previously developed the ‘chaplet column chromatography (CCC)’ method (19–22), which modified a technique for sequence-specific RNA/DNA isolation using solid-phase DNA probes (23).
[ "19–22", "23" ]
227
6,505
1
false
For efficient isolation of individual RNAs, we previously developed the ‘chaplet column chromatography (CCC)’ method, which modified a technique for sequence-specific RNA/DNA isolation using solid-phase DNA probes.
[ "19–22", "23" ]
For efficient isolation of individual RNAs, we previously developed the ‘chaplet column chromatography (CCC)’ method, which modified a technique for sequence-specific RNA/DNA isolation using solid-phase DNA probes.
true
true
true
true
true
1,072
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
The CCC method employs a DNA oligo probe complementary to each target RNA.
[ "19–22", "23" ]
74
6,506
0
false
The CCC method employs a DNA oligo probe complementary to each target RNA.
[]
The CCC method employs a DNA oligo probe complementary to each target RNA.
true
true
true
true
true
1,072
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
The DNA oligo probes are each immobilized on a resin and packed in columns which are then connected in series.
[ "19–22", "23" ]
110
6,507
0
false
The DNA oligo probes are each immobilized on a resin and packed in columns which are then connected in series.
[]
The DNA oligo probes are each immobilized on a resin and packed in columns which are then connected in series.
true
true
true
true
true
1,072
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
A solution of total RNA is circulated through the serially connected columns to entrap each target RNA.
[ "19–22", "23" ]
103
6,508
0
false
A solution of total RNA is circulated through the serially connected columns to entrap each target RNA.
[]
A solution of total RNA is circulated through the serially connected columns to entrap each target RNA.
true
true
true
true
true
1,072
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
Using this method, we successfully isolated various species of minor RNAs, such as mitochondrial tRNAs.
[ "19–22", "23" ]
103
6,509
0
false
Using this method, we successfully isolated various species of minor RNAs, such as mitochondrial tRNAs.
[]
Using this method, we successfully isolated various species of minor RNAs, such as mitochondrial tRNAs.
true
true
true
true
true
1,072
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
The CCC method, however, is still a manual, labor-intensive approach that requires significant technical expertise.
[ "19–22", "23" ]
115
6,510
0
false
The CCC method, however, is still a manual, labor-intensive approach that requires significant technical expertise.
[]
The CCC method, however, is still a manual, labor-intensive approach that requires significant technical expertise.
true
true
true
true
true
1,072
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
In addition, the high back-pressure developed by serially connecting the columns limits the degree to which this method can be scaled up.
[ "19–22", "23" ]
137
6,511
0
false
In addition, the high back-pressure developed by serially connecting the columns limits the degree to which this method can be scaled up.
[]
In addition, the high back-pressure developed by serially connecting the columns limits the degree to which this method can be scaled up.
true
true
true
true
true
1,072
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
Considering these issues for RNA isolation, we describe here a new platform technology named ‘reciprocal circulating chromatography (RCC)’ which we developed for parallel and automated affinity purification of multiple species of RNA molecules.
[ "19–22", "23" ]
244
6,512
0
false
Considering these issues for RNA isolation, we describe here a new platform technology named ‘reciprocal circulating chromatography (RCC)’ which we developed for parallel and automated affinity purification of multiple species of RNA molecules.
[]
Considering these issues for RNA isolation, we describe here a new platform technology named ‘reciprocal circulating chromatography (RCC)’ which we developed for parallel and automated affinity purification of multiple species of RNA molecules.
true
true
true
true
true
1,072
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
The most remarkable aspect of this method is that multiple RNAs are purified from a common pool of total RNA under the same conditions.
[ "19–22", "23" ]
135
6,513
0
false
The most remarkable aspect of this method is that multiple RNAs are purified from a common pool of total RNA under the same conditions.
[]
The most remarkable aspect of this method is that multiple RNAs are purified from a common pool of total RNA under the same conditions.
true
true
true
true
true
1,072
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
In addition, the RCC method is suitable for automated operation, which provides readily controllable procedures and high reproducibility.
[ "19–22", "23" ]
137
6,514
0
false
In addition, the RCC method is suitable for automated operation, which provides readily controllable procedures and high reproducibility.
[]
In addition, the RCC method is suitable for automated operation, which provides readily controllable procedures and high reproducibility.
true
true
true
true
true
1,072
2
INTRODUCTION
1
19–22
[ "B19 B20 B21 B22", "B23" ]
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
Here, we demonstrate the automated isolation of various species of ncRNAs from E. coli, yeast and mouse using a pilot RCC instrument based on an eight-channel automatic pipetting device.
[ "19–22", "23" ]
186
6,515
0
false
Here, we demonstrate the automated isolation of various species of ncRNAs from E. coli, yeast and mouse using a pilot RCC instrument based on an eight-channel automatic pipetting device.
[]
Here, we demonstrate the automated isolation of various species of ncRNAs from E. coli, yeast and mouse using a pilot RCC instrument based on an eight-channel automatic pipetting device.
true
true
true
true
true
1,072
0
DISCUSSION
1
28
[ "B28", "B29" ]
17,251,194
pmid-11733745|pmid-15539566|pmid-16141072|pmid-16651366|pmid-15372042|pmid-14744438|pmid-15211354|pmid-16751776|pmid-16751777|pmid-16882976|pmid-1594442|pmid-10429245
We have described a novel method and instrument, RCC, as a new platform technology for RNA isolation.
[ "28", "29" ]
101
6,516
0
false
We have described a novel method and instrument, RCC, as a new platform technology for RNA isolation.
[]
We have described a novel method and instrument, RCC, as a new platform technology for RNA isolation.
true
true
true
true
true
1,073
0
DISCUSSION
1
28
[ "B28", "B29" ]
17,251,194
pmid-11733745|pmid-15539566|pmid-16141072|pmid-16651366|pmid-15372042|pmid-14744438|pmid-15211354|pmid-16751776|pmid-16751777|pmid-16882976|pmid-1594442|pmid-10429245
Isolation of all species of E. coli tRNAs and various ncRNAs from yeast and mouse demonstrate that RCC is a powerful, efficient, reproducible and convenient method for isolating multiple species of RNA molecules from a single sample of total RNA.
[ "28", "29" ]
246
6,517
0
false
Isolation of all species of E. coli tRNAs and various ncRNAs from yeast and mouse demonstrate that RCC is a powerful, efficient, reproducible and convenient method for isolating multiple species of RNA molecules from a single sample of total RNA.
[]
Isolation of all species of E. coli tRNAs and various ncRNAs from yeast and mouse demonstrate that RCC is a powerful, efficient, reproducible and convenient method for isolating multiple species of RNA molecules from a single sample of total RNA.
true
true
true
true
true
1,073
0
DISCUSSION
1
28
[ "B28", "B29" ]
17,251,194
pmid-11733745|pmid-15539566|pmid-16141072|pmid-16651366|pmid-15372042|pmid-14744438|pmid-15211354|pmid-16751776|pmid-16751777|pmid-16882976|pmid-1594442|pmid-10429245
To establish this method as a generally applicable method for RNA research, it will be necessary to optimize and improve some aspects of this method.
[ "28", "29" ]
149
6,518
0
false
To establish this method as a generally applicable method for RNA research, it will be necessary to optimize and improve some aspects of this method.
[]
To establish this method as a generally applicable method for RNA research, it will be necessary to optimize and improve some aspects of this method.
true
true
true
true
true
1,073
0
DISCUSSION
1
28
[ "B28", "B29" ]
17,251,194
pmid-11733745|pmid-15539566|pmid-16141072|pmid-16651366|pmid-15372042|pmid-14744438|pmid-15211354|pmid-16751776|pmid-16751777|pmid-16882976|pmid-1594442|pmid-10429245
As shown in this study, RNA molecules were isolated with various purities and yields.
[ "28", "29" ]
85
6,519
0
false
As shown in this study, RNA molecules were isolated with various purities and yields.
[]
As shown in this study, RNA molecules were isolated with various purities and yields.
true
true
true
true
true
1,073
0
DISCUSSION
1
28
[ "B28", "B29" ]
17,251,194
pmid-11733745|pmid-15539566|pmid-16141072|pmid-16651366|pmid-15372042|pmid-14744438|pmid-15211354|pmid-16751776|pmid-16751777|pmid-16882976|pmid-1594442|pmid-10429245
These parameters depend on several factors, including probe design, temperature control and salt concentration.
[ "28", "29" ]
111
6,520
0
false
These parameters depend on several factors, including probe design, temperature control and salt concentration.
[]
These parameters depend on several factors, including probe design, temperature control and salt concentration.
true
true
true
true
true
1,073
0
DISCUSSION
1
28
[ "B28", "B29" ]
17,251,194
pmid-11733745|pmid-15539566|pmid-16141072|pmid-16651366|pmid-15372042|pmid-14744438|pmid-15211354|pmid-16751776|pmid-16751777|pmid-16882976|pmid-1594442|pmid-10429245
For isolating stable RNA molecules like tRNAs, probe design is the most important factor to achieve maximum purity and yield.
[ "28", "29" ]
125
6,521
0
false
For isolating stable RNA molecules like tRNAs, probe design is the most important factor to achieve maximum purity and yield.
[]
For isolating stable RNA molecules like tRNAs, probe design is the most important factor to achieve maximum purity and yield.
true
true
true
true
true
1,073
0
DISCUSSION
1
28
[ "B28", "B29" ]
17,251,194
pmid-11733745|pmid-15539566|pmid-16141072|pmid-16651366|pmid-15372042|pmid-14744438|pmid-15211354|pmid-16751776|pmid-16751777|pmid-16882976|pmid-1594442|pmid-10429245
Chain length, GC content and sequence specificity must also be considered for each DNA probe.
[ "28", "29" ]
93
6,522
0
false
Chain length, GC content and sequence specificity must also be considered for each DNA probe.
[]
Chain length, GC content and sequence specificity must also be considered for each DNA probe.
true
true
true
true
true
1,073
0
DISCUSSION
1
28
[ "B28", "B29" ]
17,251,194
pmid-11733745|pmid-15539566|pmid-16141072|pmid-16651366|pmid-15372042|pmid-14744438|pmid-15211354|pmid-16751776|pmid-16751777|pmid-16882976|pmid-1594442|pmid-10429245
For 44 E. coli tRNAs, we designed 30 mer DNA probes complementary to the anticodon or 3′ region of each tRNA, depending on the sequence specificity.
[ "28", "29" ]
148
6,523
0
false
For 44 E. coli tRNAs, we designed 30 mer DNA probes complementary to the anticodon or 3′ region of each tRNA, depending on the sequence specificity.
[]
For 44 E. coli tRNAs, we designed 30 mer DNA probes complementary to the anticodon or 3′ region of each tRNA, depending on the sequence specificity.
true
true
true
true
true
1,073
0
DISCUSSION
1
28
[ "B28", "B29" ]
17,251,194
pmid-11733745|pmid-15539566|pmid-16141072|pmid-16651366|pmid-15372042|pmid-14744438|pmid-15211354|pmid-16751776|pmid-16751777|pmid-16882976|pmid-1594442|pmid-10429245
To optimize design of probes for each target, northern or dot blots are convenient for checking the hybridization efficiency of each probe (28,29).
[ "28", "29" ]
147
6,524
0
false
To optimize design of probes for each target, northern or dot blots are convenient for checking the hybridization efficiency of each probe.
[ "28,29" ]
To optimize design of probes for each target, northern or dot blots are convenient for checking the hybridization efficiency of each probe.
true
true
true
true
true
1,073
0
DISCUSSION
1
28
[ "B28", "B29" ]
17,251,194
pmid-11733745|pmid-15539566|pmid-16141072|pmid-16651366|pmid-15372042|pmid-14744438|pmid-15211354|pmid-16751776|pmid-16751777|pmid-16882976|pmid-1594442|pmid-10429245
RCC might also be used to compare the efficiency and performance of several different probes for a single target RNA.
[ "28", "29" ]
117
6,525
0
false
RCC might also be used to compare the efficiency and performance of several different probes for a single target RNA.
[]
RCC might also be used to compare the efficiency and performance of several different probes for a single target RNA.
true
true
true
true
true
1,073
1
DISCUSSION
1
30
[ "B30" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
According to our theoretical model for RCC, the total yield of target RNA was closely correlated to the equilibrium constant (K ) of ligand–target interaction.
[ "30" ]
159
6,526
0
false
According to our theoretical model for RCC, the total yield of target RNA was closely correlated to the equilibrium constant (K ) of ligand–target interaction.
[]
According to our theoretical model for RCC, the total yield of target RNA was closely correlated to the equilibrium constant (K ) of ligand–target interaction.
true
true
true
true
true
1,074
1
DISCUSSION
1
30
[ "B30" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
For efficient isolation of RNA molecules, it might be better to choose nucleic-acid-related compounds as probes (30), such as the locked nucleic acid (LNA) or the peptide nucleic acid (PNA), which have higher hybridization efficiencies than a DNA probe.
[ "30" ]
253
6,527
1
false
For efficient isolation of RNA molecules, it might be better to choose nucleic-acid-related compounds as probes, such as the locked nucleic acid (LNA) or the peptide nucleic acid (PNA), which have higher hybridization efficiencies than a DNA probe.
[ "30" ]
For efficient isolation of RNA molecules, it might be better to choose nucleic-acid-related compounds as probes, such as the locked nucleic acid (LNA) or the peptide nucleic acid (PNA), which have higher hybridization efficiencies than a DNA probe.
true
true
true
true
true
1,074
1
DISCUSSION
1
30
[ "B30" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
Since a small fraction of biotinylated DNA probes detached from the streptavidin sepharose during the reciprocal circulating step, further investigation of resins and methods for immobilization of probes is needed.
[ "30" ]
214
6,528
0
false
Since a small fraction of biotinylated DNA probes detached from the streptavidin sepharose during the reciprocal circulating step, further investigation of resins and methods for immobilization of probes is needed.
[]
Since a small fraction of biotinylated DNA probes detached from the streptavidin sepharose during the reciprocal circulating step, further investigation of resins and methods for immobilization of probes is needed.
true
true
true
true
true
1,074
1
DISCUSSION
1
30
[ "B30" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
DNA probes having an amino-linker covalently bound to sepharose resin activated with N-hydroxysuccinimidyl ester may be a suitable alternative choice for immobilization.
[ "30" ]
169
6,529
0
false
DNA probes having an amino-linker covalently bound to sepharose resin activated with N-hydroxysuccinimidyl ester may be a suitable alternative choice for immobilization.
[]
DNA probes having an amino-linker covalently bound to sepharose resin activated with N-hydroxysuccinimidyl ester may be a suitable alternative choice for immobilization.
true
true
true
true
true
1,074
1
DISCUSSION
1
30
[ "B30" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
Furthermore, the temperature for hybridization and the buffer composition for each purification step is largely dependent on the particular probe.
[ "30" ]
146
6,530
0
false
Furthermore, the temperature for hybridization and the buffer composition for each purification step is largely dependent on the particular probe.
[]
Furthermore, the temperature for hybridization and the buffer composition for each purification step is largely dependent on the particular probe.
true
true
true
true
true
1,074
1
DISCUSSION
1
30
[ "B30" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
Since RCC basically has to use a single condition for 8 different probes in one operation, it is important to find conditions which are suitable for all the probes being used.
[ "30" ]
175
6,531
0
false
Since RCC basically has to use a single condition for 8 different probes in one operation, it is important to find conditions which are suitable for all the probes being used.
[]
Since RCC basically has to use a single condition for 8 different probes in one operation, it is important to find conditions which are suitable for all the probes being used.
true
true
true
true
true
1,074
1
DISCUSSION
1
30
[ "B30" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
Theoretical predictions of target RNA yield derived from a simplified model of the RCC method were closely correlated with the experimental results.
[ "30" ]
148
6,532
0
false
Theoretical predictions of target RNA yield derived from a simplified model of the RCC method were closely correlated with the experimental results.
[]
Theoretical predictions of target RNA yield derived from a simplified model of the RCC method were closely correlated with the experimental results.
true
true
true
true
true
1,074
1
DISCUSSION
1
30
[ "B30" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
The required number of cycles and yields of individual RNA species can be predicted by this model if the value of K is known.
[ "30" ]
125
6,533
0
false
The required number of cycles and yields of individual RNA species can be predicted by this model if the value of K is known.
[]
The required number of cycles and yields of individual RNA species can be predicted by this model if the value of K is known.
true
true
true
true
true
1,074
1
DISCUSSION
1
30
[ "B30" ]
17,251,194
pmid-9847178|pmid-15705854|pmid-16449203|pmid-16111943|pmid-16809489|pmid-16594986|pmid-16369484|pmid-15272117|pmid-16683135
The theoretical model is useful to optimize the conditions and operation of the RCC instrument.
[ "30" ]
95
6,534
0
false
The theoretical model is useful to optimize the conditions and operation of the RCC instrument.
[]
The theoretical model is useful to optimize the conditions and operation of the RCC instrument.
true
true
true
true
true
1,074
2
DISCUSSION
0
null
null
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
Preparation of total RNA is another critical factor for isolation of RNA species.
null
81
6,535
0
false
null
null
Preparation of total RNA is another critical factor for isolation of RNA species.
true
true
true
true
true
1,075
2
DISCUSSION
0
null
null
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
Highly concentrated total RNA provides the best starting material, especially for isolation of minor RNA species.
null
113
6,536
0
false
null
null
Highly concentrated total RNA provides the best starting material, especially for isolation of minor RNA species.
true
true
true
true
true
1,075
2
DISCUSSION
0
null
null
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
However, highly concentrated total RNA is often very viscous due to polysaccharides and other cellular components which are co-extracted from the cell.
null
151
6,537
0
false
null
null
However, highly concentrated total RNA is often very viscous due to polysaccharides and other cellular components which are co-extracted from the cell.
true
true
true
true
true
1,075
2
DISCUSSION
0
null
null
17,251,194
pmid-12456664|pmid-12554666|pmid-15781491|pmid-15477592|pmid-7985789
Prior to RCC, an initial separation of total RNA by anion exchange chromatography is required to reduce the viscosity of the concentrated total RNA solution.
null
157
6,538
0
false
null
null
Prior to RCC, an initial separation of total RNA by anion exchange chromatography is required to reduce the viscosity of the concentrated total RNA solution.
true
true
true
true
true
1,075
3
DISCUSSION
0
null
null
17,251,194
null
RCC could easily be scaled up for high throughput applications.
null
63
6,539
0
false
null
null
RCC could easily be scaled up for high throughput applications.
true
true
true
true
true
1,076
3
DISCUSSION
0
null
null
17,251,194
null
The number of channels in the RCC prototype instrument we assembled could be varied from one to eight, but a 96- or 384-channel liquid handling instrument could easily be used for RCC.
null
184
6,540
0
false
null
null
The number of channels in the RCC prototype instrument we assembled could be varied from one to eight, but a 96- or 384-channel liquid handling instrument could easily be used for RCC.
true
true
true
true
true
1,076
3
DISCUSSION
0
null
null
17,251,194
null
In such cases, the RCC instrument could be used not only as a high-throughput purification machine, but also as an analytical device for various applications in RNA research.
null
174
6,541
0
false
null
null
In such cases, the RCC instrument could be used not only as a high-throughput purification machine, but also as an analytical device for various applications in RNA research.
true
true
true
true
true
1,076
3
DISCUSSION
0
null
null
17,251,194
null
In addition, since the sample volume can be changed, minor RNA species can be purified from large volumes of an initial RNA sample, and ncRNAs such as miRNAs or piRNAs are good targets to be isolated by this method.
null
215
6,542
0
false
null
null
In addition, since the sample volume can be changed, minor RNA species can be purified from large volumes of an initial RNA sample, and ncRNAs such as miRNAs or piRNAs are good targets to be isolated by this method.
true
true
true
true
true
1,076
3
DISCUSSION
0
null
null
17,251,194
null
Most of the miRNAs are regulatively expressed in specific physiological conditions, such as pathological cells, tissues and organs.
null
131
6,543
0
false
null
null
Most of the miRNAs are regulatively expressed in specific physiological conditions, such as pathological cells, tissues and organs.
true
true
true
true
true
1,076
3
DISCUSSION
0
null
null
17,251,194
null
It is impossible to isolate each miRNA from limited quantity of specimens.
null
74
6,544
0
false
null
null
It is impossible to isolate each miRNA from limited quantity of specimens.
true
true
true
true
true
1,076
3
DISCUSSION
0
null
null
17,251,194
null
To profile miRNA expression pattern routinely, high sensitive detection systems such as microarray analysis or RT-PCR are now available.
null
136
6,545
0
false
null
null
To profile miRNA expression pattern routinely, high sensitive detection systems such as microarray analysis or RT-PCR are now available.
true
true
true
true
true
1,076
3
DISCUSSION
0
null
null
17,251,194
null
However, qualitative aspects of miRNAs are also important, because it is known that miRNAs have several dicing variants with different length and variable termini, which might modulate their activity and change its target specificity.
null
234
6,546
0
false
null
null
However, qualitative aspects of miRNAs are also important, because it is known that miRNAs have several dicing variants with different length and variable termini, which might modulate their activity and change its target specificity.
true
true
true
true
true
1,076
3
DISCUSSION
0
null
null
17,251,194
null
To investigate such qualitative information, it will be of importance to isolate each miRNA once at least (not routinely) from relatively large amount of specimen.
null
163
6,547
0
false
null
null
To investigate such qualitative information, it will be of importance to isolate each miRNA once at least (not routinely) from relatively large amount of specimen.
true
true
true
true
true
1,076
3
DISCUSSION
0
null
null
17,251,194
null
Mass spectrometry analysis of the purified RNAs can precisely quantify processing variants and/or identify the chemical structure of RNA modifications if present.
null
162
6,548
0
false
null
null
Mass spectrometry analysis of the purified RNAs can precisely quantify processing variants and/or identify the chemical structure of RNA modifications if present.
true
true
true
true
true
1,076
4
DISCUSSION
0
null
null
17,251,194
null
The RCC method can be used in a variety of applications.
null
56
6,549
0
false
null
null
The RCC method can be used in a variety of applications.
true
true
true
true
true
1,077
4
DISCUSSION
0
null
null
17,251,194
null
For example, when antibodies are immobilized on the tip-columns, RCC could be used for automated multiple-immunoprecipitations for interactome analysis.
null
152
6,550
0
false
null
null
For example, when antibodies are immobilized on the tip-columns, RCC could be used for automated multiple-immunoprecipitations for interactome analysis.
true
true
true
true
true
1,077
4
DISCUSSION
0
null
null
17,251,194
null
RCC has great potential to be used in a wide variety of applications requiring isolation of multiple components.
null
112
6,551
0
false
null
null
RCC has great potential to be used in a wide variety of applications requiring isolation of multiple components.
true
true
true
true
true
1,077
4
DISCUSSION
0
null
null
17,251,194
null
Continued refinement of the operating conditions and testing of additional applications will validate the potential of RCC.
null
123
6,552
0
false
null
null
Continued refinement of the operating conditions and testing of additional applications will validate the potential of RCC.
true
true
true
true
true
1,077
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
Bacteriophages (phages) are viruses that infect bacteria.
[ "1", "2", "3", "4", "5", "6", "7" ]
57
6,553
0
false
Bacteriophages (phages) are viruses that infect bacteria.
[]
Bacteriophages (phages) are viruses that infect bacteria.
true
true
true
true
true
1,078
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
Phages not only play important roles in the biology of their hosts, but they also have a major influence on the ecology of the oceans by cycling limiting nutrients (1) and boosting photosynthesis (2).
[ "1", "2", "3", "4", "5", "6", "7" ]
200
6,554
1
false
Phages not only play important roles in the biology of their hosts, but they also have a major influence on the ecology of the oceans by cycling limiting nutrients and boosting photosynthesis.
[ "1", "2" ]
Phages not only play important roles in the biology of their hosts, but they also have a major influence on the ecology of the oceans by cycling limiting nutrients and boosting photosynthesis.
true
true
true
true
true
1,078
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
Temperate phages (phages that integrate into the host genome) can provide essential virulence and fitness factors, affecting metabolism, bacterial adhesion, colonization, invasion, spread, resistance to immune responses, exotoxin production, serum resistance, destruction of competing bacteria and resistance to antibiot...
[ "1", "2", "3", "4", "5", "6", "7" ]
330
6,555
0
false
Temperate phages (phages that integrate into the host genome) can provide essential virulence and fitness factors, affecting metabolism, bacterial adhesion, colonization, invasion, spread, resistance to immune responses, exotoxin production, serum resistance, destruction of competing bacteria and resistance to antibiot...
[ "3,4" ]
Temperate phages (phages that integrate into the host genome) can provide essential virulence and fitness factors, affecting metabolism, bacterial adhesion, colonization, invasion, spread, resistance to immune responses, exotoxin production, serum resistance, destruction of competing bacteria and resistance to antibiot...
true
true
true
true
true
1,078
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
These capabilities can be generated by the introduction of novel genes or by altering expression of existing genes.
[ "1", "2", "3", "4", "5", "6", "7" ]
115
6,556
0
false
These capabilities can be generated by the introduction of novel genes or by altering expression of existing genes.
[]
These capabilities can be generated by the introduction of novel genes or by altering expression of existing genes.
true
true
true
true
true
1,078
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
Phages have also contributed significantly to our understanding of many cellular processes and have been a source of countless enzymes used routinely in molecular biology and biotechnology.
[ "1", "2", "3", "4", "5", "6", "7" ]
189
6,557
0
false
Phages have also contributed significantly to our understanding of many cellular processes and have been a source of countless enzymes used routinely in molecular biology and biotechnology.
[]
Phages have also contributed significantly to our understanding of many cellular processes and have been a source of countless enzymes used routinely in molecular biology and biotechnology.
true
true
true
true
true
1,078
0
INTRODUCTION
1
5
[ "b1", "b2", "b3", "b4", "b5", "b6", "b7" ]
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
Furthermore, phages themselves (5) or proteins produced by them (6,7) may be used as antimicrobials to cure bacterial infections in humans and are being developed as household disinfectants.
[ "1", "2", "3", "4", "5", "6", "7" ]
190
6,558
1
false
Furthermore, phages themselves or proteins produced by them may be used as antimicrobials to cure bacterial infections in humans and are being developed as household disinfectants.
[ "5", "6,7" ]
Furthermore, phages themselves or proteins produced by them may be used as antimicrobials to cure bacterial infections in humans and are being developed as household disinfectants.
true
true
true
true
true
1,078
1
INTRODUCTION
1
8
[ "b8", "b9" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
More than 5000 phages have been classified since 1959 by electron microscopy (8), yet <3% of these have been completely sequenced and deposited in public databanks.
[ "8", "9" ]
164
6,559
1
false
More than 5000 phages have been classified since 1959 by electron microscopy, yet <3% of these have been completely sequenced and deposited in public databanks.
[ "8" ]
More than 5000 phages have been classified since 1959 by electron microscopy, yet <3% of these have been completely sequenced and deposited in public databanks.
true
true
true
true
true
1,079
1
INTRODUCTION
1
9
[ "b8", "b9" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
Considering the estimate of ∼1030 phages in the world (9), the diversity of phages is likely to be great which means more complete phage genome sequences will be needed to fully comprehend the true extent of genetic diversity, the capacity for genetic mobilization/exchange and the evolution of bacteriophages.
[ "8", "9" ]
310
6,560
1
false
Considering the estimate of ∼1030 phages in the world, the diversity of phages is likely to be great which means more complete phage genome sequences will be needed to fully comprehend the true extent of genetic diversity, the capacity for genetic mobilization/exchange and the evolution of bacteriophages.
[ "9" ]
Considering the estimate of ∼1030 phages in the world, the diversity of phages is likely to be great which means more complete phage genome sequences will be needed to fully comprehend the true extent of genetic diversity, the capacity for genetic mobilization/exchange and the evolution of bacteriophages.
true
true
true
true
true
1,079
1
INTRODUCTION
1
8
[ "b8", "b9" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
Until this happens, there is an enormous, poorly explored, publicly available resource of bacteriophage genomes within the complete sequence of bacterial genomes.
[ "8", "9" ]
162
6,561
0
false
Until this happens, there is an enormous, poorly explored, publicly available resource of bacteriophage genomes within the complete sequence of bacterial genomes.
[]
Until this happens, there is an enormous, poorly explored, publicly available resource of bacteriophage genomes within the complete sequence of bacterial genomes.
true
true
true
true
true
1,079
1
INTRODUCTION
1
8
[ "b8", "b9" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
The phage genomes that can be recovered in this way are the double-stranded DNA tailed phages in the order
[ "8", "9" ]
106
6,562
0
false
The phage genomes that can be recovered in this way are the double-stranded DNA tailed phages in the order
[]
The phage genomes that can be recovered in this way are the double-stranded DNA tailed phages in the order
true
true
false
true
false
1,079
1
INTRODUCTION
1
8
[ "b8", "b9" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
Caudovirales and single-stranded DNA filamentous phages in the order Inoviridae that are known to integrate into the genome of their host.
[ "8", "9" ]
138
6,563
0
false
Caudovirales and single-stranded DNA filamentous phages in the order Inoviridae that are known to integrate into the genome of their host.
[]
Caudovirales and single-stranded DNA filamentous phages in the order Inoviridae that are known to integrate into the genome of their host.
true
true
true
true
true
1,079
2
INTRODUCTION
1
10
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Current bacterial genome sequencing projects poorly identify and annotate regions of bacteriophage origin and there are no standard definitions for the classification of these regions.
[ "10", "11", "12" ]
184
6,564
0
false
Current bacterial genome sequencing projects poorly identify and annotate regions of bacteriophage origin and there are no standard definitions for the classification of these regions.
[]
Current bacterial genome sequencing projects poorly identify and annotate regions of bacteriophage origin and there are no standard definitions for the classification of these regions.
true
true
true
true
true
1,080
2
INTRODUCTION
1
10
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
There are multiple reasons for this.
[ "10", "11", "12" ]
36
6,565
0
false
There are multiple reasons for this.
[]
There are multiple reasons for this.
true
true
true
true
true
1,080
2
INTRODUCTION
1
10
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Many groups identify phage regions by manual inspection (10).
[ "10", "11", "12" ]
61
6,566
1
false
Many groups identify phage regions by manual inspection.
[ "10" ]
Many groups identify phage regions by manual inspection.
true
true
true
true
true
1,080
2
INTRODUCTION
1
10
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Some consider any region with matches to phage sequence a prophage, while others have a more stringent definition and require complete or nearly complete sets of phage genes within the region to be considered a prophage.
[ "10", "11", "12" ]
220
6,567
0
false
Some consider any region with matches to phage sequence a prophage, while others have a more stringent definition and require complete or nearly complete sets of phage genes within the region to be considered a prophage.
[]
Some consider any region with matches to phage sequence a prophage, while others have a more stringent definition and require complete or nearly complete sets of phage genes within the region to be considered a prophage.
true
true
true
true
true
1,080
2
INTRODUCTION
1
10
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
The annotation of the genes within these regions is even more variable because each group has different criteria for gene annotation.
[ "10", "11", "12" ]
133
6,568
0
false
The annotation of the genes within these regions is even more variable because each group has different criteria for gene annotation.
[]
The annotation of the genes within these regions is even more variable because each group has different criteria for gene annotation.
true
true
true
true
true
1,080
2
INTRODUCTION
1
10
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
One of the greatest problems with the identification of prophage regions is the enormous diversity within the phage population, which can be observed in the sequence of many of the complete phage genomes where >50% of open reading frames (ORFs) have no database match.
[ "10", "11", "12" ]
268
6,569
0
false
One of the greatest problems with the identification of prophage regions is the enormous diversity within the phage population, which can be observed in the sequence of many of the complete phage genomes where >50% of open reading frames (ORFs) have no database match.
[]
One of the greatest problems with the identification of prophage regions is the enormous diversity within the phage population, which can be observed in the sequence of many of the complete phage genomes where >50% of open reading frames (ORFs) have no database match.
true
true
true
true
true
1,080
2
INTRODUCTION
1
10
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Another problem is that some regions are not complete phages, but just contain mainly tail fibers and lytic enzymes that have been hijacked by the host and used as weaponry to fight off competitors.
[ "10", "11", "12" ]
198
6,570
0
false
Another problem is that some regions are not complete phages, but just contain mainly tail fibers and lytic enzymes that have been hijacked by the host and used as weaponry to fight off competitors.
[]
Another problem is that some regions are not complete phages, but just contain mainly tail fibers and lytic enzymes that have been hijacked by the host and used as weaponry to fight off competitors.
true
true
true
true
true
1,080
2
INTRODUCTION
1
10
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
These regions would be considered bacteriocins and have been called by many different names, depending on the species of origin (i.e.
[ "10", "11", "12" ]
133
6,571
0
false
These regions would be considered bacteriocins and have been called by many different names, depending on the species of origin (i.e.
[]
These regions would be considered bacteriocins and have been called by many different names, depending on the species of origin (i.e.
true
true
true
true
true
1,080
2
INTRODUCTION
1
11
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
monocin for Listeria monocytogenes, pyocin for Pseudomonas aeruginosa) (11).
[ "10", "11", "12" ]
76
6,572
1
false
monocin for Listeria monocytogenes, pyocin for Pseudomonas aeruginosa).
[ "11" ]
monocin for Listeria monocytogenes, pyocin for Pseudomonas aeruginosa).
false
true
true
true
false
1,080
2
INTRODUCTION
1
10
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Some investigators try to rely on altered G + C content of the region or the disruption of genes (particularly, the targeting or tRNAs) as methods of defining the boundaries of prophage regions.
[ "10", "11", "12" ]
194
6,573
0
false
Some investigators try to rely on altered G + C content of the region or the disruption of genes (particularly, the targeting or tRNAs) as methods of defining the boundaries of prophage regions.
[]
Some investigators try to rely on altered G + C content of the region or the disruption of genes (particularly, the targeting or tRNAs) as methods of defining the boundaries of prophage regions.
true
true
true
true
true
1,080
2
INTRODUCTION
1
12
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
We have shown that prophage regions do not always have atypical G + C nucleotide composition (12), so this is not a reliable method.
[ "10", "11", "12" ]
132
6,574
1
false
We have shown that prophage regions do not always have atypical G + C nucleotide composition, so this is not a reliable method.
[ "12" ]
We have shown that prophage regions do not always have atypical G + C nucleotide composition, so this is not a reliable method.
true
true
true
true
true
1,080
2
INTRODUCTION
1
10
[ "b10", "b11", "b12" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Phages do not always integrate into coding regions and do not exclusively use tRNAs as the target site for integration, making scanning for disrupted genes or tRNAs as a standalone method inadequate for finding prophage regions.
[ "10", "11", "12" ]
228
6,575
0
false
Phages do not always integrate into coding regions and do not exclusively use tRNAs as the target site for integration, making scanning for disrupted genes or tRNAs as a standalone method inadequate for finding prophage regions.
[]
Phages do not always integrate into coding regions and do not exclusively use tRNAs as the target site for integration, making scanning for disrupted genes or tRNAs as a standalone method inadequate for finding prophage regions.
true
true
true
true
true
1,080
3
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
Phage_Finder was developed as a heuristic computer program to identify prophage regions within bacterial genomes and is freely available ( or ).
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
144
6,576
0
false
Phage_Finder was developed as a heuristic computer program to identify prophage regions within bacterial genomes and is freely available ( or ).
[]
Phage_Finder was developed as a heuristic computer program to identify prophage regions within bacterial genomes and is freely available ( or ).
true
true
true
true
true
1,081
3
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
It uses tab-delimited results from NCBI BLASTALL (13) or WU BLASTP 2.0 () (14) searches against a collection of bacteriophage sequences and results from HMMSEARCH (15) analysis of 441 phage-specific hidden Markov models (HMMs) to locate prophage regions.
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
254
6,577
1
false
It uses tab-delimited results from NCBI BLASTALL or WU BLASTP 2.0 () searches against a collection of bacteriophage sequences and results from HMMSEARCH analysis of 441 phage-specific hidden Markov models (HMMs) to locate prophage regions.
[ "13", "14", "15" ]
It uses tab-delimited results from NCBI BLASTALL or WU BLASTP 2.0 () searches against a collection of bacteriophage sequences and results from HMMSEARCH analysis of 441 phage-specific hidden Markov models (HMMs) to locate prophage regions.
true
true
true
true
true
1,081
3
INTRODUCTION
1
14
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
By using FASTA33 (16), MUMMER (17) or BLASTN (14), it can find potential attachment (att) sites of the phage region(s).
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
119
6,578
1
false
By using FASTA33, MUMMER or BLASTN, it can find potential attachment (att) sites of the phage region(s).
[ "16", "17", "14" ]
By using FASTA33, MUMMER or BLASTN, it can find potential attachment (att) sites of the phage region(s).
true
true
true
true
true
1,081
3
INTRODUCTION
1
18
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
Data from tRNAscan-SE (18) and Aragorn (19) are used to determine whether a tRNA or tmRNA served as the putative target for integration.
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
136
6,579
1
false
Data from tRNAscan-SE and Aragorn are used to determine whether a tRNA or tmRNA served as the putative target for integration.
[ "18", "19" ]
Data from tRNAscan-SE and Aragorn are used to determine whether a tRNA or tmRNA served as the putative target for integration.
true
true
true
true
true
1,081
3
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
Additionally, by looking for the presence or absence of specific proteins using HMMs, Phage_Finder can predict whether the region is most likely prophage and which type (Mu, P2, or retron R73), an integrated element, a plasmid, or a degenerate phage region.
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
257
6,580
0
false
Additionally, by looking for the presence or absence of specific proteins using HMMs, Phage_Finder can predict whether the region is most likely prophage and which type (Mu, P2, or retron R73), an integrated element, a plasmid, or a degenerate phage region.
[]
Additionally, by looking for the presence or absence of specific proteins using HMMs, Phage_Finder can predict whether the region is most likely prophage and which type, an integrated element, a plasmid, or a degenerate phage region.
true
true
true
true
true
1,081
3
INTRODUCTION
1
20
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
The pipeline was tested against a set of manually-defined prophage regions (20).
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
80
6,581
1
false
The pipeline was tested against a set of manually-defined prophage regions.
[ "20" ]
The pipeline was tested against a set of manually-defined prophage regions.
true
true
true
true
true
1,081
3
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
Phage_Finder found 91% of these regions, resulting in 7% false positives and 9% false negatives with a test dataset using default settings (Table 2).
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
149
6,582
0
false
Phage_Finder found 91% of these regions, resulting in 7% false positives and 9% false negatives with a test dataset using default settings (Table 2).
[]
Phage_Finder found 91% of these regions, resulting in 7% false positives and 9% false negatives with a test dataset using default settings (Table 2).
true
true
true
true
true
1,081
3
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
To test the robustness of the pipeline, 302 complete bacterial genomes were processed through the pipeline.
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
107
6,583
0
false
To test the robustness of the pipeline, 302 complete bacterial genomes were processed through the pipeline.
[]
To test the robustness of the pipeline, 302 complete bacterial genomes were processed through the pipeline.
true
true
true
true
true
1,081
3
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
A total of 403 putative prophage regions were identified, which accounted for 1.7% of the total bacterial DNA.
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
110
6,584
0
false
A total of 403 putative prophage regions were identified, which accounted for 1.7% of the total bacterial DNA.
[]
A total of 403 putative prophage regions were identified, which accounted for 1.7% of the total bacterial DNA.
true
true
true
true
true
1,081
3
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
In addition to finding prophage regions, Phage_Finder has found integrated elements and integrated plasmids.
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
108
6,585
0
false
In addition to finding prophage regions, Phage_Finder has found integrated elements and integrated plasmids.
[]
In addition to finding prophage regions, Phage_Finder has found integrated elements and integrated plasmids.
true
true
true
true
true
1,081
3
INTRODUCTION
1
13
[ "b13", "b14", "b15", "b16", "b17", "b14", "b18", "b19", "b20" ]
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
A novel method for constructing phylogenetic trees of phages and prophages was developed based on the mean of the BLAST score ratio (BSR) of bacteriophage proteins.
[ "13", "14", "15", "16", "17", "14", "18", "19", "20" ]
164
6,586
0
false
A novel method for constructing phylogenetic trees of phages and prophages was developed based on the mean of the BLAST score ratio (BSR) of bacteriophage proteins.
[]
A novel method for constructing phylogenetic trees of phages and prophages was developed based on the mean of the BLAST score ratio (BSR) of bacteriophage proteins.
true
true
true
true
true
1,081
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
A software package has been described that searches complete bacterial genomes for the presence of bacteriophage-like regions and generates several output files.
null
161
6,587
0
false
null
null
A software package has been described that searches complete bacterial genomes for the presence of bacteriophage-like regions and generates several output files.
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
To test the accuracy of prediction, the program was ran against a set of 42 complete bacterial genomes that had manually curated prophages with putative attachment sites.
null
170
6,588
0
false
null
null
To test the accuracy of prediction, the program was ran against a set of 42 complete bacterial genomes that had manually curated prophages with putative attachment sites.
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
Phage_Finder found all but 11 manually identified prophage regions.
null
67
6,589
0
false
null
null
Phage_Finder found all but 11 manually identified prophage regions.
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
The missed regions fall into one of two categories (regions that did not meet the ‘strict’ definition and regions that have more than one prophage integrated into the same attachment site in tandom—so called ‘piggy-back’ prophages).
null
232
6,590
0
false
null
null
The missed regions fall into one of two categories (regions that did not meet the ‘strict’ definition and regions that have more than one prophage integrated into the same attachment site in tandom—so called ‘piggy-back’ prophages).
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
The piggy-back phage regions were either fused into one large region or truncated.
null
82
6,591
0
false
null
null
The piggy-back phage regions were either fused into one large region or truncated.
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
It is difficult for the program to tease these regions apart because there are multiple possible attachment sites (one pair marking the boundary of the first prophage and another pair marking the boundary of the entire tandem series).
null
234
6,592
0
false
null
null
It is difficult for the program to tease these regions apart because there are multiple possible attachment sites (one pair marking the boundary of the first prophage and another pair marking the boundary of the entire tandem series).
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
Since this happens infrequently (3% of the test dataset), future updates to the program will deal with this issue.
null
114
6,593
0
false
null
null
Since this happens infrequently (3% of the test dataset), future updates to the program will deal with this issue.
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
There are still many putative prophage regions that do not have core HMM matches (large terminase, portal, major capsid), which could be the reason why some of the manually identified prophages were missed under the strict mode.
null
228
6,594
0
false
null
null
There are still many putative prophage regions that do not have core HMM matches (large terminase, portal, major capsid), which could be the reason why some of the manually identified prophages were missed under the strict mode.
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
As more HMMs are built to these important phage proteins, the robustness of phage detection will increase.
null
106
6,595
0
false
null
null
As more HMMs are built to these important phage proteins, the robustness of phage detection will increase.
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
The accuracy of boundary prediction was measured by calculating the difference in ORF counts (between the known and predict prophage regions) per bacterial genome (17 ORFs/genome, Table 2).
null
189
6,596
0
false
null
null
The accuracy of boundary prediction was measured by calculating the difference in ORF counts (between the known and predict prophage regions) per bacterial genome (17 ORFs/genome, Table 2).
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
Currently, the program chooses between one of the two top matches to either a tRNA sequence or the sequence extending 400 bp outside of the integrase gene.
null
155
6,597
0
false
null
null
Currently, the program chooses between one of the two top matches to either a tRNA sequence or the sequence extending 400 bp outside of the integrase gene.
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
If the query sequence is a tRNA, then the longest att site is chosen, but if the query sequence was from near the integrase gene, then a different strategy is taken.
null
165
6,598
0
false
null
null
If the query sequence is a tRNA, then the longest att site is chosen, but if the query sequence was from near the integrase gene, then a different strategy is taken.
true
true
true
true
true
1,082
0
DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
The best att site is determined as one that is either in the 3′ end of a gene or has the longest length.
null
104
6,599
0
false
null
null
The best att site is determined as one that is either in the 3′ end of a gene or has the longest length.
true
true
true
true
true
1,082