Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
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2
INTRODUCTION
1
9
[ "B9", "B10 B11 B12", "B13", "B14", "B15", "B16", "B16" ]
17,311,815
pmid-2565038|pmid-369706|pmid-10380764|pmid-11385705|pmid-11524730|pmid-9600452|pmid-15141034|pmid-12177413|pmid-12177413
Chemical differences can also be utilized for SNP detection.
[ "9", "10–12", "13", "14", "15", "16", "16" ]
60
5,900
0
false
Chemical differences can also be utilized for SNP detection.
[]
Chemical differences can also be utilized for SNP detection.
true
true
true
true
true
980
2
INTRODUCTION
1
13
[ "B9", "B10 B11 B12", "B13", "B14", "B15", "B16", "B16" ]
17,311,815
pmid-2565038|pmid-369706|pmid-10380764|pmid-11385705|pmid-11524730|pmid-9600452|pmid-15141034|pmid-12177413|pmid-12177413
In principle, any reagent that specifically recognizes and cleaves mismatched DNA can be used for the detection (13), and heteroduplex-cleaving chemicals (14) or proteins (15) have been used for the purpose.
[ "9", "10–12", "13", "14", "15", "16", "16" ]
207
5,901
1
false
In principle, any reagent that specifically recognizes and cleaves mismatched DNA can be used for the detection, and heteroduplex-cleaving chemicals or proteins have been used for the purpose.
[ "13", "14", "15" ]
In principle, any reagent that specifically recognizes and cleaves mismatched DNA can be used for the detection, and heteroduplex-cleaving chemicals or proteins have been used for the purpose.
true
true
true
true
true
980
2
INTRODUCTION
1
16
[ "B9", "B10 B11 B12", "B13", "B14", "B15", "B16", "B16" ]
17,311,815
pmid-2565038|pmid-369706|pmid-10380764|pmid-11385705|pmid-11524730|pmid-9600452|pmid-15141034|pmid-12177413|pmid-12177413
Recently, a novel DNA-cleaving reagent became available when it was shown that Mu transposition preferentially targets mismatched sites in DNA (16).
[ "9", "10–12", "13", "14", "15", "16", "16" ]
148
5,902
1
false
Recently, a novel DNA-cleaving reagent became available when it was shown that Mu transposition preferentially targets mismatched sites in DNA.
[ "16" ]
Recently, a novel DNA-cleaving reagent became available when it was shown that Mu transposition preferentially targets mismatched sites in DNA.
true
true
true
true
true
980
2
INTRODUCTION
1
16
[ "B9", "B10 B11 B12", "B13", "B14", "B15", "B16", "B16" ]
17,311,815
pmid-2565038|pmid-369706|pmid-10380764|pmid-11385705|pmid-11524730|pmid-9600452|pmid-15141034|pmid-12177413|pmid-12177413
This proof of principle study established the mismatch-targeting methodology and indicated, using a known polymorphic test fragment, that mutations indeed can be detected by the use of transposon approach (16).
[ "9", "10–12", "13", "14", "15", "16", "16" ]
210
5,903
1
false
This proof of principle study established the mismatch-targeting methodology and indicated, using a known polymorphic test fragment, that mutations indeed can be detected by the use of transposon approach.
[ "16" ]
This proof of principle study established the mismatch-targeting methodology and indicated, using a known polymorphic test fragment, that mutations indeed can be detected by the use of transposon approach.
true
true
true
true
true
980
3
INTRODUCTION
1
17
[ "B17", "B18", "B19" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
The present study has been stimulated by research on the Glanville fritillary butterfly (Melitaea cinxia).
[ "17", "18", "19" ]
106
5,904
0
false
The present study has been stimulated by research on the Glanville fritillary butterfly (Melitaea cinxia).
[]
The present study has been stimulated by research on the Glanville fritillary butterfly (Melitaea cinxia).
true
true
true
true
true
981
3
INTRODUCTION
1
17
[ "B17", "B18", "B19" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
This species and its large metapopulation in Finland have become a much-studied model system in population biology (17).
[ "17", "18", "19" ]
120
5,905
1
false
This species and its large metapopulation in Finland have become a much-studied model system in population biology.
[ "17" ]
This species and its large metapopulation in Finland have become a much-studied model system in population biology.
true
true
true
true
true
981
3
INTRODUCTION
1
17
[ "B17", "B18", "B19" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
Adding a strong genetic component into the existing ecological context would be highly desirable, but the paucity of suitable genetic markers has hampered the progress towards this goal.
[ "17", "18", "19" ]
186
5,906
0
false
Adding a strong genetic component into the existing ecological context would be highly desirable, but the paucity of suitable genetic markers has hampered the progress towards this goal.
[]
Adding a strong genetic component into the existing ecological context would be highly desirable, but the paucity of suitable genetic markers has hampered the progress towards this goal.
true
true
true
true
true
981
3
INTRODUCTION
1
18
[ "B17", "B18", "B19" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
In particular, the development of effective microsatellite markers for Lepidoptera species, including M. cinxia, has turned out to be difficult (18).
[ "17", "18", "19" ]
149
5,907
1
false
In particular, the development of effective microsatellite markers for Lepidoptera species, including M. cinxia, has turned out to be difficult.
[ "18" ]
In particular, the development of effective microsatellite markers for Lepidoptera species, including M. cinxia, has turned out to be difficult.
true
true
true
true
true
981
3
INTRODUCTION
1
19
[ "B17", "B18", "B19" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
Possible reasons for this may involve a high degree of variation close to the microsatellite loci as well as the presence of duplicated genomic regions or several copies of mobile elements (19).
[ "17", "18", "19" ]
194
5,908
1
false
Possible reasons for this may involve a high degree of variation close to the microsatellite loci as well as the presence of duplicated genomic regions or several copies of mobile elements.
[ "19" ]
Possible reasons for this may involve a high degree of variation close to the microsatellite loci as well as the presence of duplicated genomic regions or several copies of mobile elements.
true
true
true
true
true
981
3
INTRODUCTION
1
17
[ "B17", "B18", "B19" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
Considering the above difficulties, other types of genetic markers are needed, and for many purposes SNPs represent an attractive alternative.
[ "17", "18", "19" ]
142
5,909
0
false
Considering the above difficulties, other types of genetic markers are needed, and for many purposes SNPs represent an attractive alternative.
[]
Considering the above difficulties, other types of genetic markers are needed, and for many purposes SNPs represent an attractive alternative.
true
true
true
true
true
981
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
Here, we adopted the methodology of Mu transposition to detect mismatches in DNA (16) and developed a strategy to isolate SNP markers from uncharted genomes.
[ "16", "20", "21", "20", "22–27", "16" ]
157
5,910
1
false
Here, we adopted the methodology of Mu transposition to detect mismatches in DNA and developed a strategy to isolate SNP markers from uncharted genomes.
[ "16" ]
Here, we adopted the methodology of Mu transposition to detect mismatches in DNA and developed a strategy to isolate SNP markers from uncharted genomes.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
The methodology exploits the bacteriophage Mu DNA transposition machinery, the critical components of which include a tetramer of MuA transposase and two transposon end segments (20,21).
[ "16", "20", "21", "20", "22–27", "16" ]
186
5,911
0
false
The methodology exploits the bacteriophage Mu DNA transposition machinery, the critical components of which include a tetramer of MuA transposase and two transposon end segments.
[ "20,21" ]
The methodology exploits the bacteriophage Mu DNA transposition machinery, the critical components of which include a tetramer of MuA transposase and two transposon end segments.
true
true
true
true
true
982
4
INTRODUCTION
1
20
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
The assembly of this machinery and subsequent transposase-catalyzed reaction steps (Figure 1A) can be reconstituted in a simple in vitro reaction that includes transposon DNA (a short Mu genome right-end segment suffices), MuA transposase and target DNA as the only macromolecular components (20).
[ "16", "20", "21", "20", "22–27", "16" ]
297
5,912
1
false
The assembly of this machinery and subsequent transposase-catalyzed reaction steps (Figure 1A) can be reconstituted in a simple in vitro reaction that includes transposon DNA (a short Mu genome right-end segment suffices), MuA transposase and target DNA as the only macromolecular components.
[ "20" ]
The assembly of this machinery and subsequent transposase-catalyzed reaction steps (Figure 1A) can be reconstituted in a simple in vitro reaction that includes transposon DNA (a short Mu genome right-end segment suffices), MuA transposase and target DNA as the only macromolecular components.
true
true
true
true
true
982
4
INTRODUCTION
1
22–27
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
This minimal in vitro reaction has recently been used in a number of advanced molecular biology, protein engineering and genomics applications (22–27), and it has become evident that many other novel applications can be tackled with this technology.
[ "16", "20", "21", "20", "22–27", "16" ]
249
5,913
1
false
This minimal in vitro reaction has recently been used in a number of advanced molecular biology, protein engineering and genomics applications, and it has become evident that many other novel applications can be tackled with this technology.
[ "22–27" ]
This minimal in vitro reaction has recently been used in a number of advanced molecular biology, protein engineering and genomics applications, and it has become evident that many other novel applications can be tackled with this technology.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
Figure 1.Mismatch targeting of Mu transposition.
[ "16", "20", "21", "20", "22–27", "16" ]
48
5,914
0
false
Figure 1.Mismatch targeting of Mu transposition.
[]
Figure 1.Mismatch targeting of Mu transposition.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
(A) Outline of the Mu transpositional recombination steps used in this study.
[ "16", "20", "21", "20", "22–27", "16" ]
77
5,915
0
false
(A) Outline of the Mu transpositional recombination steps used in this study.
[]
(A) Outline of the Mu transpositional recombination steps used in this study.
false
false
true
true
false
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
MuA transposase protein assembles two transposon end segments into a tetrameric DNA transposition complex.
[ "16", "20", "21", "20", "22–27", "16" ]
106
5,916
0
false
MuA transposase protein assembles two transposon end segments into a tetrameric DNA transposition complex.
[]
MuA transposase protein assembles two transposon end segments into a tetrameric DNA transposition complex.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
This complex captures the target DNA and executes the strand transfer reaction, during which the transposon DNA is joined into the target in a concerted reaction involving a 5-bp stagger, and the target DNA strands are simultaneously cleaved.
[ "16", "20", "21", "20", "22–27", "16" ]
242
5,917
0
false
This complex captures the target DNA and executes the strand transfer reaction, during which the transposon DNA is joined into the target in a concerted reaction involving a 5-bp stagger, and the target DNA strands are simultaneously cleaved.
[]
This complex captures the target DNA and executes the strand transfer reaction, during which the transposon DNA is joined into the target in a concerted reaction involving a 5-bp stagger, and the target DNA strands are simultaneously cleaved.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
R1 and R2 (rectangles) denote MuA transposase-binding sites.
[ "16", "20", "21", "20", "22–27", "16" ]
60
5,918
0
false
R1 and R2 (rectangles) denote MuA transposase-binding sites.
[]
R1 and R2 (rectangles) denote MuA transposase-binding sites.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
The arrows indicate the 5-bp staggered locations for strand transfer on the two strands.
[ "16", "20", "21", "20", "22–27", "16" ]
88
5,919
0
false
The arrows indicate the 5-bp staggered locations for strand transfer on the two strands.
[]
The arrows indicate the 5-bp staggered locations for strand transfer on the two strands.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
When mismatched sites are present in the target DNA, nearly 90% of the strand transfers occur at these sites (16).
[ "16", "20", "21", "20", "22–27", "16" ]
114
5,920
1
false
When mismatched sites are present in the target DNA, nearly 90% of the strand transfers occur at these sites.
[ "16" ]
When mismatched sites are present in the target DNA, nearly 90% of the strand transfers occur at these sites.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
(B) If genomic DNA contains at least two alleles within a specified DNA region, amplification of that region by PCR produces DNA duplexes that contain mismatches.
[ "16", "20", "21", "20", "22–27", "16" ]
162
5,921
0
false
(B) If genomic DNA contains at least two alleles within a specified DNA region, amplification of that region by PCR produces DNA duplexes that contain mismatches.
[]
(B) If genomic DNA contains at least two alleles within a specified DNA region, amplification of that region by PCR produces DNA duplexes that contain mismatches.
false
false
true
true
false
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
Such a situation arises when the region is amplified from a heterozygous individual or from a sample that combines DNA from two or more individuals representing different allelic variants.
[ "16", "20", "21", "20", "22–27", "16" ]
188
5,922
0
false
Such a situation arises when the region is amplified from a heterozygous individual or from a sample that combines DNA from two or more individuals representing different allelic variants.
[]
Such a situation arises when the region is amplified from a heterozygous individual or from a sample that combines DNA from two or more individuals representing different allelic variants.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
In this example, mismatched nucleotides are shown in bold.
[ "16", "20", "21", "20", "22–27", "16" ]
58
5,923
0
false
In this example, mismatched nucleotides are shown in bold.
[]
In this example, mismatched nucleotides are shown in bold.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
(C) Lengths of the DNA strands within the transposition product.
[ "16", "20", "21", "20", "22–27", "16" ]
64
5,924
0
false
(C) Lengths of the DNA strands within the transposition product.
[]
(C) Lengths of the DNA strands within the transposition product.
false
false
true
true
false
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
Transposon DNA is shown in black and target DNA in gray.
[ "16", "20", "21", "20", "22–27", "16" ]
56
5,925
0
false
Transposon DNA is shown in black and target DNA in gray.
[]
Transposon DNA is shown in black and target DNA in gray.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
Numbers indicate known lengths (in nucleotides), and labeled reaction products are indicated with asterisks.
[ "16", "20", "21", "20", "22–27", "16" ]
108
5,926
0
false
Numbers indicate known lengths (in nucleotides), and labeled reaction products are indicated with asterisks.
[]
Numbers indicate known lengths (in nucleotides), and labeled reaction products are indicated with asterisks.
true
true
true
true
true
982
4
INTRODUCTION
1
16
[ "B16", "B20", "B21", "B20", "B22 B23 B24 B25 B26 B27", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
Two formulas for the calculation of the product lengths are shown at the bottom.
[ "16", "20", "21", "20", "22–27", "16" ]
80
5,927
0
false
Two formulas for the calculation of the product lengths are shown at the bottom.
[]
Two formulas for the calculation of the product lengths are shown at the bottom.
true
true
true
true
true
982
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
Mismatch targeting of Mu transposition.
[ "16" ]
39
5,928
0
false
Mismatch targeting of Mu transposition.
[]
Mismatch targeting of Mu transposition.
true
true
true
true
true
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
(A) Outline of the Mu transpositional recombination steps used in this study.
[ "16" ]
77
5,929
0
false
(A) Outline of the Mu transpositional recombination steps used in this study.
[]
(A) Outline of the Mu transpositional recombination steps used in this study.
false
false
true
true
false
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
MuA transposase protein assembles two transposon end segments into a tetrameric DNA transposition complex.
[ "16" ]
106
5,930
0
false
MuA transposase protein assembles two transposon end segments into a tetrameric DNA transposition complex.
[]
MuA transposase protein assembles two transposon end segments into a tetrameric DNA transposition complex.
true
true
true
true
true
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
This complex captures the target DNA and executes the strand transfer reaction, during which the transposon DNA is joined into the target in a concerted reaction involving a 5-bp stagger, and the target DNA strands are simultaneously cleaved.
[ "16" ]
242
5,931
0
false
This complex captures the target DNA and executes the strand transfer reaction, during which the transposon DNA is joined into the target in a concerted reaction involving a 5-bp stagger, and the target DNA strands are simultaneously cleaved.
[]
This complex captures the target DNA and executes the strand transfer reaction, during which the transposon DNA is joined into the target in a concerted reaction involving a 5-bp stagger, and the target DNA strands are simultaneously cleaved.
true
true
true
true
true
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
R1 and R2 (rectangles) denote MuA transposase-binding sites.
[ "16" ]
60
5,932
0
false
R1 and R2 (rectangles) denote MuA transposase-binding sites.
[]
R1 and R2 (rectangles) denote MuA transposase-binding sites.
true
true
true
true
true
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
The arrows indicate the 5-bp staggered locations for strand transfer on the two strands.
[ "16" ]
88
5,933
0
false
The arrows indicate the 5-bp staggered locations for strand transfer on the two strands.
[]
The arrows indicate the 5-bp staggered locations for strand transfer on the two strands.
true
true
true
true
true
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
When mismatched sites are present in the target DNA, nearly 90% of the strand transfers occur at these sites (16).
[ "16" ]
114
5,934
1
false
When mismatched sites are present in the target DNA, nearly 90% of the strand transfers occur at these sites.
[ "16" ]
When mismatched sites are present in the target DNA, nearly 90% of the strand transfers occur at these sites.
true
true
true
true
true
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
(B) If genomic DNA contains at least two alleles within a specified DNA region, amplification of that region by PCR produces DNA duplexes that contain mismatches.
[ "16" ]
162
5,935
0
false
(B) If genomic DNA contains at least two alleles within a specified DNA region, amplification of that region by PCR produces DNA duplexes that contain mismatches.
[]
(B) If genomic DNA contains at least two alleles within a specified DNA region, amplification of that region by PCR produces DNA duplexes that contain mismatches.
false
false
true
true
false
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
Such a situation arises when the region is amplified from a heterozygous individual or from a sample that combines DNA from two or more individuals representing different allelic variants.
[ "16" ]
188
5,936
0
false
Such a situation arises when the region is amplified from a heterozygous individual or from a sample that combines DNA from two or more individuals representing different allelic variants.
[]
Such a situation arises when the region is amplified from a heterozygous individual or from a sample that combines DNA from two or more individuals representing different allelic variants.
true
true
true
true
true
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
In this example, mismatched nucleotides are shown in bold.
[ "16" ]
58
5,937
0
false
In this example, mismatched nucleotides are shown in bold.
[]
In this example, mismatched nucleotides are shown in bold.
true
true
true
true
true
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
(C) Lengths of the DNA strands within the transposition product.
[ "16" ]
64
5,938
0
false
(C) Lengths of the DNA strands within the transposition product.
[]
(C) Lengths of the DNA strands within the transposition product.
false
false
true
true
false
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
Transposon DNA is shown in black and target DNA in gray.
[ "16" ]
56
5,939
0
false
Transposon DNA is shown in black and target DNA in gray.
[]
Transposon DNA is shown in black and target DNA in gray.
true
true
true
true
true
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
Numbers indicate known lengths (in nucleotides), and labeled reaction products are indicated with asterisks.
[ "16" ]
108
5,940
0
false
Numbers indicate known lengths (in nucleotides), and labeled reaction products are indicated with asterisks.
[]
Numbers indicate known lengths (in nucleotides), and labeled reaction products are indicated with asterisks.
true
true
true
true
true
983
5
INTRODUCTION
1
16
[ "B16" ]
17,311,815
pmid-12177413
Two formulas for the calculation of the product lengths are shown at the bottom.
[ "16" ]
80
5,941
0
false
Two formulas for the calculation of the product lengths are shown at the bottom.
[]
Two formulas for the calculation of the product lengths are shown at the bottom.
true
true
true
true
true
983
0
DISCUSSION
1
5
[ "B5", "B4" ]
17,311,815
pmid-9872978|pmid-16255080|pmid-11726933|NA|pmid-15660941|pmid-15660941|NA
Single nucleotide polymorphisms provide the markers of choice for evolutionary, ecological and conservation studies (5).
[ "5", "4" ]
120
5,942
1
false
Single nucleotide polymorphisms provide the markers of choice for evolutionary, ecological and conservation studies.
[ "5" ]
Single nucleotide polymorphisms provide the markers of choice for evolutionary, ecological and conservation studies.
true
true
true
true
true
984
0
DISCUSSION
1
4
[ "B5", "B4" ]
17,311,815
pmid-9872978|pmid-16255080|pmid-11726933|NA|pmid-15660941|pmid-15660941|NA
The ease with which SNP data can be modeled as well as the abundance of SNPs in genomes make them ideal for the study of population histories (4).
[ "5", "4" ]
146
5,943
1
false
The ease with which SNP data can be modeled as well as the abundance of SNPs in genomes make them ideal for the study of population histories.
[ "4" ]
The ease with which SNP data can be modeled as well as the abundance of SNPs in genomes make them ideal for the study of population histories.
true
true
true
true
true
984
0
DISCUSSION
1
5
[ "B5", "B4" ]
17,311,815
pmid-9872978|pmid-16255080|pmid-11726933|NA|pmid-15660941|pmid-15660941|NA
A major limiting factor for their use for non-model organisms in population biology has been the lack of an efficient and cost-effective method to isolate new markers.
[ "5", "4" ]
167
5,944
0
false
A major limiting factor for their use for non-model organisms in population biology has been the lack of an efficient and cost-effective method to isolate new markers.
[]
A major limiting factor for their use for non-model organisms in population biology has been the lack of an efficient and cost-effective method to isolate new markers.
true
true
true
true
true
984
0
DISCUSSION
1
5
[ "B5", "B4" ]
17,311,815
pmid-9872978|pmid-16255080|pmid-11726933|NA|pmid-15660941|pmid-15660941|NA
The mismatch-targeting of Mu transposition-based strategy described in this article has the potential to solve this problem.
[ "5", "4" ]
124
5,945
0
false
The mismatch-targeting of Mu transposition-based strategy described in this article has the potential to solve this problem.
[]
The mismatch-targeting of Mu transposition-based strategy described in this article has the potential to solve this problem.
true
true
true
true
true
984
0
DISCUSSION
1
5
[ "B5", "B4" ]
17,311,815
pmid-9872978|pmid-16255080|pmid-11726933|NA|pmid-15660941|pmid-15660941|NA
Important for many researchers in population genetics and evolutionary biology, this method requires no special facilities over standard molecular biology laboratory.
[ "5", "4" ]
166
5,946
0
false
Important for many researchers in population genetics and evolutionary biology, this method requires no special facilities over standard molecular biology laboratory.
[]
Important for many researchers in population genetics and evolutionary biology, this method requires no special facilities over standard molecular biology laboratory.
true
true
true
true
true
984
1
DISCUSSION
1
35
[ "B35", "B36" ]
17,311,815
pmid-15829236|pmid-15379655|pmid-15676075|pmid-8675443|NA
The present methodology involves undemanding cloning and sequencing steps, yielding data for the design of genome-specific primers.
[ "35", "36" ]
131
5,947
0
false
The present methodology involves undemanding cloning and sequencing steps, yielding data for the design of genome-specific primers.
[]
The present methodology involves undemanding cloning and sequencing steps, yielding data for the design of genome-specific primers.
true
true
true
true
true
985
1
DISCUSSION
1
35
[ "B35", "B36" ]
17,311,815
pmid-15829236|pmid-15379655|pmid-15676075|pmid-8675443|NA
In this study, a third of the designed primer pairs amplified a single PCR product, and the rest of them failed in amplification or amplified several products.
[ "35", "36" ]
159
5,948
0
false
In this study, a third of the designed primer pairs amplified a single PCR product, and the rest of them failed in amplification or amplified several products.
[]
In this study, a third of the designed primer pairs amplified a single PCR product, and the rest of them failed in amplification or amplified several products.
true
true
true
true
true
985
1
DISCUSSION
1
35
[ "B35", "B36" ]
17,311,815
pmid-15829236|pmid-15379655|pmid-15676075|pmid-8675443|NA
While some of the amplification problems may have been caused by sub-optimally designed primer pairs, we suspect that some of these failures may reflect substantial variation among individuals and/or stretches of sequence similarity in different loci.
[ "35", "36" ]
251
5,949
0
false
While some of the amplification problems may have been caused by sub-optimally designed primer pairs, we suspect that some of these failures may reflect substantial variation among individuals and/or stretches of sequence similarity in different loci.
[]
While some of the amplification problems may have been caused by sub-optimally designed primer pairs, we suspect that some of these failures may reflect substantial variation among individuals and/or stretches of sequence similarity in different loci.
true
true
true
true
true
985
1
DISCUSSION
1
35
[ "B35", "B36" ]
17,311,815
pmid-15829236|pmid-15379655|pmid-15676075|pmid-8675443|NA
In general, variation within primer-binding sites may influence the amplification, and large indels are expected to generate several fragments.
[ "35", "36" ]
143
5,950
0
false
In general, variation within primer-binding sites may influence the amplification, and large indels are expected to generate several fragments.
[]
In general, variation within primer-binding sites may influence the amplification, and large indels are expected to generate several fragments.
true
true
true
true
true
985
1
DISCUSSION
1
35
[ "B35", "B36" ]
17,311,815
pmid-15829236|pmid-15379655|pmid-15676075|pmid-8675443|NA
In addition, duplicated or otherwise similar but not identical genome regions as well as multiple copies of mobile elements can generate a complex set of amplification products.
[ "35", "36" ]
177
5,951
0
false
In addition, duplicated or otherwise similar but not identical genome regions as well as multiple copies of mobile elements can generate a complex set of amplification products.
[]
In addition, duplicated or otherwise similar but not identical genome regions as well as multiple copies of mobile elements can generate a complex set of amplification products.
true
true
true
true
true
985
1
DISCUSSION
1
35
[ "B35", "B36" ]
17,311,815
pmid-15829236|pmid-15379655|pmid-15676075|pmid-8675443|NA
The fact that a high percentage of primer pairs generated multiple PCR products or failed to generate products in our study may relate to the exceptional difficulties encountered in the development of microsatellite markers for Lepidoptera species, including the Glanville fritillary.
[ "35", "36" ]
284
5,952
0
false
The fact that a high percentage of primer pairs generated multiple PCR products or failed to generate products in our study may relate to the exceptional difficulties encountered in the development of microsatellite markers for Lepidoptera species, including the Glanville fritillary.
[]
The fact that a high percentage of primer pairs generated multiple PCR products or failed to generate products in our study may relate to the exceptional difficulties encountered in the development of microsatellite markers for Lepidoptera species, including the Glanville fritillary.
true
true
true
true
true
985
1
DISCUSSION
1
35
[ "B35", "B36" ]
17,311,815
pmid-15829236|pmid-15379655|pmid-15676075|pmid-8675443|NA
Indeed, a high level of variation within the flanking regions of microsatellites has hampered their use as markers (35,36).
[ "35", "36" ]
123
5,953
0
false
Indeed, a high level of variation within the flanking regions of microsatellites has hampered their use as markers.
[ "35,36" ]
Indeed, a high level of variation within the flanking regions of microsatellites has hampered their use as markers.
true
true
true
true
true
985
2
DISCUSSION
0
null
null
17,311,815
pmid-2565038|pmid-369706|pmid-10380764|pmid-11385705|pmid-11524730|pmid-9600452|pmid-15141034|pmid-12177413|pmid-12177413
Fragment length appears not to be very critical for the present methodology, as in a preliminary phase of this study, DNA fragments up to 1.3 kb in size were successfully analyzed for the presence of variation in the Glanville fritillary (data not shown).
null
255
5,954
0
false
null
null
Fragment length appears not to be very critical for the present methodology, as in a preliminary phase of this study, DNA fragments up to 1.3 kb in size were successfully analyzed for the presence of variation in the Glanville fritillary (data not shown).
true
true
true
true
true
986
2
DISCUSSION
0
null
null
17,311,815
pmid-2565038|pmid-369706|pmid-10380764|pmid-11385705|pmid-11524730|pmid-9600452|pmid-15141034|pmid-12177413|pmid-12177413
Thereafter, most of the analyzed butterfly DNA fragments were targeted to fall within the 250–350-bp size range for convenience: such fragments are short enough for straightforward genomic amplification, sequencing can be accomplished with one primer and optimal separation of transposition reaction products is achieved...
null
321
5,955
0
false
null
null
Thereafter, most of the analyzed butterfly DNA fragments were targeted to fall within the 250–350-bp size range for convenience: such fragments are short enough for straightforward genomic amplification, sequencing can be accomplished with one primer and optimal separation of transposition reaction products is achieved...
true
true
true
true
true
986
2
DISCUSSION
0
null
null
17,311,815
pmid-2565038|pmid-369706|pmid-10380764|pmid-11385705|pmid-11524730|pmid-9600452|pmid-15141034|pmid-12177413|pmid-12177413
Nevertheless, as shown with model DNA fragments (Figure S1), a single mismatched nucleotide pair can readily be detected even when it is present in a 2-kb fragment.
null
164
5,956
0
false
null
null
Nevertheless, as shown with model DNA fragments (Figure S1), a single mismatched nucleotide pair can readily be detected even when it is present in a 2-kb fragment.
true
true
true
true
true
986
3
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
Mu mismatch-targeting can be easily visualized by the use of electrophoresis and autoradiography.
[ "16", "16" ]
97
5,957
0
false
Mu mismatch-targeting can be easily visualized by the use of electrophoresis and autoradiography.
[]
Mu mismatch-targeting can be easily visualized by the use of electrophoresis and autoradiography.
true
true
true
true
true
987
3
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
The two transposon ends integrate simultaneously into each of the target DNA strands (Figure 1A), generating two complementary products (Figure 1C).
[ "16", "16" ]
148
5,958
0
false
The two transposon ends integrate simultaneously into each of the target DNA strands (Figure 1A), generating two complementary products (Figure 1C).
[]
The two transposon ends integrate simultaneously into each of the target DNA strands, generating two complementary products.
true
true
true
true
true
987
3
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
Hence, the symmetrical banding pattern in autoradiographs serves as a built-in quality measure, discriminating against any potential artifacts.
[ "16", "16" ]
143
5,959
0
false
Hence, the symmetrical banding pattern in autoradiographs serves as a built-in quality measure, discriminating against any potential artifacts.
[]
Hence, the symmetrical banding pattern in autoradiographs serves as a built-in quality measure, discriminating against any potential artifacts.
true
true
true
true
true
987
3
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
The lengths of the transposition reaction products can be estimated with a reasonable accuracy by the use of molecular size markers, although a degree of sequence-specific variation in migration does exist among single-strands.
[ "16", "16" ]
227
5,960
0
false
The lengths of the transposition reaction products can be estimated with a reasonable accuracy by the use of molecular size markers, although a degree of sequence-specific variation in migration does exist among single-strands.
[]
The lengths of the transposition reaction products can be estimated with a reasonable accuracy by the use of molecular size markers, although a degree of sequence-specific variation in migration does exist among single-strands.
true
true
true
true
true
987
3
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
NA|pmid-10931678|pmid-15140111|pmid-12177413|pmid-12177413
In most cases, the targeted mismatch is located in the middle of the 5-bp target region core (16), generating easily interpretable banding patterns (Figure 1C, Table S5), although some targeting into nearby nucleotides may also occur (16).
[ "16", "16" ]
239
5,961
2
true
In most cases, the targeted mismatch is located in the middle of the 5-bp target region core, generating easily interpretable banding patterns (Figure 1C, Table S5), although some targeting into nearby nucleotides may also occur.
[ "16", "16" ]
In most cases, the targeted mismatch is located in the middle of the 5-bp target region core, generating easily interpretable banding patterns, although some targeting into nearby nucleotides may also occur.
true
true
true
true
true
987
4
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
We found that Mu-mediated integration can detect many, but not necessarily all, SNPs present within a particular DNA fragment.
[ "16", "16" ]
126
5,962
0
false
We found that Mu-mediated integration can detect many, but not necessarily all, SNPs present within a particular DNA fragment.
[]
We found that Mu-mediated integration can detect many, but not necessarily all, SNPs present within a particular DNA fragment.
true
true
true
true
true
988
4
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
Thus, the autoradiographic data will underestimate the actual variation in cases where many variable nucleotides are present within a single genomic fragment.
[ "16", "16" ]
158
5,963
0
false
Thus, the autoradiographic data will underestimate the actual variation in cases where many variable nucleotides are present within a single genomic fragment.
[]
Thus, the autoradiographic data will underestimate the actual variation in cases where many variable nucleotides are present within a single genomic fragment.
true
true
true
true
true
988
4
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
As the exact targeting mechanism of Mu transposition is currently not known, it is unclear why some sites are less effective than others, and what might be the maximum number of simultaneously identifiable mismatched sites within a given fragment.
[ "16", "16" ]
247
5,964
0
false
As the exact targeting mechanism of Mu transposition is currently not known, it is unclear why some sites are less effective than others, and what might be the maximum number of simultaneously identifiable mismatched sites within a given fragment.
[]
As the exact targeting mechanism of Mu transposition is currently not known, it is unclear why some sites are less effective than others, and what might be the maximum number of simultaneously identifiable mismatched sites within a given fragment.
true
true
true
true
true
988
4
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
A suggestion that the machinery samples a large number of potential target sites before integration (16) is consistent with our data, but the mechanism of the site-discrimination process remains to be elucidated.
[ "16", "16" ]
212
5,965
1
false
A suggestion that the machinery samples a large number of potential target sites before integration is consistent with our data, but the mechanism of the site-discrimination process remains to be elucidated.
[ "16" ]
A suggestion that the machinery samples a large number of potential target sites before integration is consistent with our data, but the mechanism of the site-discrimination process remains to be elucidated.
true
true
true
true
true
988
4
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
Remarkably, the Mu machinery can mediate transposition at detectable levels into a mismatched site in the presence of 300 000-fold excess of non-mismatch sites, and all single nucleotide mismatch types as well as longer mismatches (at least up to 5 nt) target efficiently (16).
[ "16", "16" ]
277
5,966
1
false
Remarkably, the Mu machinery can mediate transposition at detectable levels into a mismatched site in the presence of 300 000-fold excess of non-mismatch sites, and all single nucleotide mismatch types as well as longer mismatches (at least up to 5 nt) target efficiently.
[ "16" ]
Remarkably, the Mu machinery can mediate transposition at detectable levels into a mismatched site in the presence of 300 000-fold excess of non-mismatch sites, and all single nucleotide mismatch types as well as longer mismatches (at least up to 5 nt) target efficiently.
true
true
true
true
true
988
4
DISCUSSION
1
16
[ "B16", "B16" ]
17,311,815
pmid-12177413|pmid-7588618|pmid-15774720|pmid-7588618|pmid-10373596|pmid-10077537|pmid-11932242|pmid-14997564|pmid-16006618|pmid-12477817|pmid-12177413|pmid-12177413|pmid-12177413
In summary, the currently available data (16, this study) suggest that Mu transposition never fails to detect a single mismatch within a fragment, and some mismatches may become non-detectable only in fragments where they are present in a combination with those that can be detected, generating favorable circumstances f...
[ "16", "16" ]
337
5,967
0
false
In summary, the currently available data suggest that Mu transposition never fails to detect a single mismatch within a fragment, and some mismatches may become non-detectable only in fragments where they are present in a combination with those that can be detected, generating favorable circumstances for SNP discovery.
[ "16, this study" ]
In summary, the currently available data suggest that Mu transposition never fails to detect a single mismatch within a fragment, and some mismatches may become non-detectable only in fragments where they are present in a combination with those that can be detected, generating favorable circumstances for SNP discovery.
true
true
true
true
true
988
5
DISCUSSION
0
null
null
17,311,815
pmid-12177413
The Mu-mediated SNP discovery process discriminates effectively against invariant regions and detects variation-containing fragments with 100% efficiency.
null
154
5,968
0
false
null
null
The Mu-mediated SNP discovery process discriminates effectively against invariant regions and detects variation-containing fragments with 100% efficiency.
true
true
true
true
true
989
5
DISCUSSION
0
null
null
17,311,815
pmid-12177413
Therefore, sequencing can be focused on those regions where one will surely find polymorphic sites, thus avoiding massive and expensive sequencing efforts.
null
155
5,969
0
false
null
null
Therefore, sequencing can be focused on those regions where one will surely find polymorphic sites, thus avoiding massive and expensive sequencing efforts.
true
true
true
true
true
989
5
DISCUSSION
0
null
null
17,311,815
pmid-12177413
On the other hand, too much variation is often problematic for primer probe design, and such problems can be avoided by choosing for sequencing only those fragments that show relatively few bands in the autoradiograph.
null
218
5,970
0
false
null
null
On the other hand, too much variation is often problematic for primer probe design, and such problems can be avoided by choosing for sequencing only those fragments that show relatively few bands in the autoradiograph.
true
true
true
true
true
989
5
DISCUSSION
0
null
null
17,311,815
pmid-12177413
Here, we selected 13 fragments with different degrees of variation, two of which were too variable for primer probe design.
null
123
5,971
0
false
null
null
Here, we selected 13 fragments with different degrees of variation, two of which were too variable for primer probe design.
true
true
true
true
true
989
6
DISCUSSION
1
6
[ "B6", "B7" ]
17,311,815
pmid-15829236|pmid-15379655
Another advantage of the present methodology is the possibility to label the transposon DNA, alleviating the need to label each target fragment separately.
[ "6", "7" ]
155
5,972
0
false
Another advantage of the present methodology is the possibility to label the transposon DNA, alleviating the need to label each target fragment separately.
[]
Another advantage of the present methodology is the possibility to label the transposon DNA, alleviating the need to label each target fragment separately.
true
true
true
true
true
990
6
DISCUSSION
1
6
[ "B6", "B7" ]
17,311,815
pmid-15829236|pmid-15379655
Although we used radioactive labeling, non-radioactive protocols could be applicable as well.
[ "6", "7" ]
93
5,973
0
false
Although we used radioactive labeling, non-radioactive protocols could be applicable as well.
[]
Although we used radioactive labeling, non-radioactive protocols could be applicable as well.
true
true
true
true
true
990
6
DISCUSSION
1
6
[ "B6", "B7" ]
17,311,815
pmid-15829236|pmid-15379655
The benefit is that the labeled transposon reagent could be stored for extended periods of time for future use.
[ "6", "7" ]
111
5,974
0
false
The benefit is that the labeled transposon reagent could be stored for extended periods of time for future use.
[]
The benefit is that the labeled transposon reagent could be stored for extended periods of time for future use.
true
true
true
true
true
990
6
DISCUSSION
1
6
[ "B6", "B7" ]
17,311,815
pmid-15829236|pmid-15379655
The lack of apparent fragment size upper limit as such and the possibility to locate mutations with certain accuracy are clear advantages over methods that rely on conformational differences (SSCP and DGGE, see ref.
[ "6", "7" ]
215
5,975
0
false
The lack of apparent fragment size upper limit as such and the possibility to locate mutations with certain accuracy are clear advantages over methods that rely on conformational differences (SSCP and DGGE, see ref.
[]
The lack of apparent fragment size upper limit as such and the possibility to locate mutations with certain accuracy are clear advantages over methods that rely on conformational differences (SSCP and DGGE, see ref.
true
true
true
true
true
990
6
DISCUSSION
1
6
[ "B6", "B7" ]
17,311,815
pmid-15829236|pmid-15379655
37 and references therein).
[ "6", "7" ]
27
5,976
0
false
37 and references therein).
[]
37 and references therein).
false
false
true
true
false
990
6
DISCUSSION
1
6
[ "B6", "B7" ]
17,311,815
pmid-15829236|pmid-15379655
However, with longer DNA fragments, gel resolution becomes a more pronounced issue, but similar problems apply to all methodologies that require resolution of different length DNA molecules.
[ "6", "7" ]
190
5,977
0
false
However, with longer DNA fragments, gel resolution becomes a more pronounced issue, but similar problems apply to all methodologies that require resolution of different length DNA molecules.
[]
However, with longer DNA fragments, gel resolution becomes a more pronounced issue, but similar problems apply to all methodologies that require resolution of different length DNA molecules.
true
true
true
true
true
990
6
DISCUSSION
1
6
[ "B6", "B7" ]
17,311,815
pmid-15829236|pmid-15379655
Also, the presence of indels may complicate the analysis, but this is a common problem among almost all currently available methods, excluding certain direct DNA sequencing approaches (6,7).
[ "6", "7" ]
190
5,978
0
false
Also, the presence of indels may complicate the analysis, but this is a common problem among almost all currently available methods, excluding certain direct DNA sequencing approaches.
[ "6,7" ]
Also, the presence of indels may complicate the analysis, but this is a common problem among almost all currently available methods, excluding certain direct DNA sequencing approaches.
true
true
true
true
true
990
7
DISCUSSION
1
38
[ "B38", "B39" ]
17,311,815
pmid-9753726|pmid-15948293
Of the currently available techniques, those that rely on enzymatic DNA cleavage agents, such as CEL I (38,39), are most closely related to the described Mu strategy.
[ "38", "39" ]
166
5,979
0
false
Of the currently available techniques, those that rely on enzymatic DNA cleavage agents, such as CEL I, are most closely related to the described Mu strategy.
[ "38,39" ]
Of the currently available techniques, those that rely on enzymatic DNA cleavage agents, such as CEL I, are most closely related to the described Mu strategy.
true
true
true
true
true
991
7
DISCUSSION
1
38
[ "B38", "B39" ]
17,311,815
pmid-9753726|pmid-15948293
Yet, certain key differences exist.
[ "38", "39" ]
35
5,980
0
false
Yet, certain key differences exist.
[]
Yet, certain key differences exist.
true
true
true
true
true
991
7
DISCUSSION
1
38
[ "B38", "B39" ]
17,311,815
pmid-9753726|pmid-15948293
In comparison to CEL I, Mu methodology does not require labeling of the target DNA; therefore, the labeling costs are minimized.
[ "38", "39" ]
128
5,981
0
false
In comparison to CEL I, Mu methodology does not require labeling of the target DNA; therefore, the labeling costs are minimized.
[]
In comparison to CEL I, Mu methodology does not require labeling of the target DNA; therefore, the labeling costs are minimized.
true
true
true
true
true
991
7
DISCUSSION
1
38
[ "B38", "B39" ]
17,311,815
pmid-9753726|pmid-15948293
The reaction products of CEL I cleavage are shorter than the labeled (target) DNA substrate.
[ "38", "39" ]
92
5,982
0
false
The reaction products of CEL I cleavage are shorter than the labeled (target) DNA substrate.
[]
The reaction products of CEL I cleavage are shorter than the labeled (target) DNA substrate.
true
true
true
true
true
991
7
DISCUSSION
1
38
[ "B38", "B39" ]
17,311,815
pmid-9753726|pmid-15948293
In contrast, the Mu methodology generates labeled products that are longer than the labeled (donor) DNA substrate, yielding favorable circumstances with regard to the signal to noise ratio.
[ "38", "39" ]
189
5,983
0
false
In contrast, the Mu methodology generates labeled products that are longer than the labeled (donor) DNA substrate, yielding favorable circumstances with regard to the signal to noise ratio.
[]
In contrast, the Mu methodology generates labeled products that are longer than the labeled (donor) DNA substrate, yielding favorable circumstances with regard to the signal to noise ratio.
true
true
true
true
true
991
7
DISCUSSION
1
38
[ "B38", "B39" ]
17,311,815
pmid-9753726|pmid-15948293
(iii) The detection of mutations very close to the ends of fragments is difficult with enzymatic mutation detection technologies, including CEL I.
[ "38", "39" ]
146
5,984
0
false
(iii) The detection of mutations very close to the ends of fragments is difficult with enzymatic mutation detection technologies, including CEL I.
[]
(iii) The detection of mutations very close to the ends of fragments is difficult with enzymatic mutation detection technologies, including CEL I.
false
false
true
true
false
991
7
DISCUSSION
1
38
[ "B38", "B39" ]
17,311,815
pmid-9753726|pmid-15948293
Because the Mu transposition product contains 51 extra nucleotides derived from the donor DNA (Figure 1), mutations located close to the end of the fragment are detectable by standard gel assays.
[ "38", "39" ]
195
5,985
0
false
Because the Mu transposition product contains 51 extra nucleotides derived from the donor DNA (Figure 1), mutations located close to the end of the fragment are detectable by standard gel assays.
[]
Because the Mu transposition product contains 51 extra nucleotides derived from the donor DNA (Figure 1), mutations located close to the end of the fragment are detectable by standard gel assays.
true
true
true
true
true
991
8
DISCUSSION
1
40
[ "B40", "B41" ]
17,311,815
pmid-1736283|pmid-15864324
The methodology we describe here functions robustly, but some improvements may be envisioned.
[ "40", "41" ]
93
5,986
0
false
The methodology we describe here functions robustly, but some improvements may be envisioned.
[]
The methodology we describe here functions robustly, but some improvements may be envisioned.
true
true
true
true
true
992
8
DISCUSSION
1
40
[ "B40", "B41" ]
17,311,815
pmid-1736283|pmid-15864324
For example, the initial cloning step may not be necessary, as arbitrary priming and linker ligation-mediated protocols for genomic amplification are available (40,41).
[ "40", "41" ]
168
5,987
0
false
For example, the initial cloning step may not be necessary, as arbitrary priming and linker ligation-mediated protocols for genomic amplification are available.
[ "40,41" ]
For example, the initial cloning step may not be necessary, as arbitrary priming and linker ligation-mediated protocols for genomic amplification are available.
true
true
true
true
true
992
8
DISCUSSION
1
40
[ "B40", "B41" ]
17,311,815
pmid-1736283|pmid-15864324
We purified the genomic PCR fragments by the use of chromatography, but any PCR purification method should be applicable.
[ "40", "41" ]
121
5,988
0
false
We purified the genomic PCR fragments by the use of chromatography, but any PCR purification method should be applicable.
[]
We purified the genomic PCR fragments by the use of chromatography, but any PCR purification method should be applicable.
true
true
true
true
true
992
8
DISCUSSION
1
40
[ "B40", "B41" ]
17,311,815
pmid-1736283|pmid-15864324
In fact, we tested one commercial kit (see Methods) for the purpose and the results compared favorably with those obtained with chromatographically purified fragments.
[ "40", "41" ]
167
5,989
0
false
In fact, we tested one commercial kit (see Methods) for the purpose and the results compared favorably with those obtained with chromatographically purified fragments.
[]
In fact, we tested one commercial kit (see Methods) for the purpose and the results compared favorably with those obtained with chromatographically purified fragments.
true
true
true
true
true
992
8
DISCUSSION
1
40
[ "B40", "B41" ]
17,311,815
pmid-1736283|pmid-15864324
In addition, many types of advanced technologies, including capillary electrophoresis and automation to generate a high-throughput environment, could be linked with the present methodology.
[ "40", "41" ]
189
5,990
0
false
In addition, many types of advanced technologies, including capillary electrophoresis and automation to generate a high-throughput environment, could be linked with the present methodology.
[]
In addition, many types of advanced technologies, including capillary electrophoresis and automation to generate a high-throughput environment, could be linked with the present methodology.
true
true
true
true
true
992
8
DISCUSSION
1
40
[ "B40", "B41" ]
17,311,815
pmid-1736283|pmid-15864324
Considering the numerous advantages, the mismatch-targeting of Mu transposition-based strategy described in this paper has the potential to become the favored approach to develop SNP markers for non-model organisms.
[ "40", "41" ]
215
5,991
0
false
Considering the numerous advantages, the mismatch-targeting of Mu transposition-based strategy described in this paper has the potential to become the favored approach to develop SNP markers for non-model organisms.
[]
Considering the numerous advantages, the mismatch-targeting of Mu transposition-based strategy described in this paper has the potential to become the favored approach to develop SNP markers for non-model organisms.
true
true
true
true
true
992
0
INTRODUCTION
1
1
[ "b1", "b4" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
Evolution is the result of variation and selection of the components and structure of organisms through time.
[ "1", "4" ]
109
5,992
0
false
Evolution is the result of variation and selection of the components and structure of organisms through time.
[]
Evolution is the result of variation and selection of the components and structure of organisms through time.
true
true
true
true
true
993
0
INTRODUCTION
1
1
[ "b1", "b4" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
Transcriptional regulation plays a prominent role in the expression of genetic information.
[ "1", "4" ]
91
5,993
0
false
Transcriptional regulation plays a prominent role in the expression of genetic information.
[]
Transcriptional regulation plays a prominent role in the expression of genetic information.
true
true
true
true
true
993
0
INTRODUCTION
1
1
[ "b1", "b4" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
Its primary role in microbial organisms is controlling the response to environmental changes, such as nutritional status and several stresses.
[ "1", "4" ]
142
5,994
0
false
Its primary role in microbial organisms is controlling the response to environmental changes, such as nutritional status and several stresses.
[]
Its primary role in microbial organisms is controlling the response to environmental changes, such as nutritional status and several stresses.
true
true
true
true
true
993
0
INTRODUCTION
1
1
[ "b1", "b4" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
An important idea emerging in post-genomic biology is that transcriptional regulation can be viewed as a complex network of interactions among diverse types of molecules like proteins, DNA and metabolites (1–4).
[ "1", "4" ]
211
5,995
0
false
An important idea emerging in post-genomic biology is that transcriptional regulation can be viewed as a complex network of interactions among diverse types of molecules like proteins, DNA and metabolites.
[ "1–4" ]
An important idea emerging in post-genomic biology is that transcriptional regulation can be viewed as a complex network of interactions among diverse types of molecules like proteins, DNA and metabolites.
true
true
true
true
true
993
0
INTRODUCTION
1
1
[ "b1", "b4" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
In this work we try to assess the evolution of the structure and plasticity of the transcriptional regulatory network (TRN) across species at three distinct levels: individual components of the TRN, pairs of regulatory interactions and regulons [A regulon is defined as the group of all genes regulated by a transcriptio...
[ "1", "4" ]
335
5,996
0
false
In this work we try to assess the evolution of the structure and plasticity of the transcriptional regulatory network (TRN) across species at three distinct levels: individual components of the TRN, pairs of regulatory interactions and regulons [A regulon is defined as the group of all genes regulated by a transcriptio...
[]
In this work we try to assess the evolution of the structure and plasticity of the transcriptional regulatory network (TRN) across species at three distinct levels: individual components of the TRN, pairs of regulatory interactions and regulons [A regulon is defined as the group of all genes regulated by a transcriptio...
true
true
false
true
false
993
0
INTRODUCTION
1
1
[ "b1", "b4" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
, through a comparative analysis of their conservation.
[ "1", "4" ]
55
5,997
0
false
, through a comparative analysis of their conservation.
[]
, through a comparative analysis of their conservation.
false
false
true
true
false
993
1
INTRODUCTION
1
5
[ "b5", "b7" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
The basic unit of gene regulatory interaction consists of three components: a TF, its DNA-binding site (operator) and the target gene (TG).
[ "5", "7" ]
139
5,998
0
false
The basic unit of gene regulatory interaction consists of three components: a TF, its DNA-binding site (operator) and the target gene (TG).
[]
The basic unit of gene regulatory interaction consists of three components: a TF, its DNA-binding site (operator) and the target gene (TG).
true
true
true
true
true
994
1
INTRODUCTION
1
5
[ "b5", "b7" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
Topologically, the TRN is complex because genes may be regulated by more than one TF and some TFs may control more than one gene through DNA-binding site(s) (5–7).
[ "5", "7" ]
163
5,999
0
false
Topologically, the TRN is complex because genes may be regulated by more than one TF and some TFs may control more than one gene through DNA-binding site(s).
[ "5–7" ]
Topologically, the TRN is complex because genes may be regulated by more than one TF and some TFs may control more than one gene through DNA-binding site(s).
true
true
true
true
true
994