Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
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cites
string
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sentences
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sentence_batch_index
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DISCUSSION
0
null
null
17,062,630
pmid-12944965|pmid-12917674|pmid-12117903|pmid-16585764|pmid-12399562|pmid-12192412|pmid-14716317
Future updates will likely focus on a more sophisticated strategy for attachment site prediction, since the longest att site is not necessarily the one used by the phage integrase.
null
180
6,600
0
false
null
null
Future updates will likely focus on a more sophisticated strategy for attachment site prediction, since the longest att site is not necessarily the one used by the phage integrase.
true
true
true
true
true
1,082
1
DISCUSSION
1
27
[ "b27" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
Never before the creation of this tool has it been possible to analyze such a large dataset of prophage sequences (447 prophage or prophage regions encoding 6171 proteins).
[ "27" ]
172
6,601
0
false
Never before the creation of this tool has it been possible to analyze such a large dataset of prophage sequences (447 prophage or prophage regions encoding 6171 proteins).
[]
Never before the creation of this tool has it been possible to analyze such a large dataset of prophage sequences.
true
true
true
true
true
1,083
1
DISCUSSION
1
27
[ "b27" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
Initial studies of the data in this report looked at the distribution of 285 putative attachment sites (Figure 2) and the distribution of 679 phages, prophages and predicted prophages (Figure 4).
[ "27" ]
195
6,602
0
false
Initial studies of the data in this report looked at the distribution of 285 putative attachment sites (Figure 2) and the distribution of 679 phages, prophages and predicted prophages (Figure 4).
[]
Initial studies of the data in this report looked at the distribution of 285 putative attachment sites and the distribution of 679 phages, prophages and predicted prophages (Figure 4).
true
true
true
true
true
1,083
1
DISCUSSION
1
27
[ "b27" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
From data presented in Figure 2, it was concluded that tRNAs, intergenic and intragenic regions are targeted with about the same frequency (roughly a third of the time).
[ "27" ]
169
6,603
0
false
From data presented in Figure 2, it was concluded that tRNAs, intergenic and intragenic regions are targeted with about the same frequency (roughly a third of the time).
[]
From data presented in Figure 2, it was concluded that tRNAs, intergenic and intragenic regions are targeted with about the same frequency (roughly a third of the time).
true
true
true
true
true
1,083
1
DISCUSSION
1
27
[ "b27" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
tmRNAs were targeted infrequently at 8% of the time.
[ "27" ]
52
6,604
0
false
tmRNAs were targeted infrequently at 8% of the time.
[]
tmRNAs were targeted infrequently at 8% of the time.
false
true
true
true
false
1,083
1
DISCUSSION
1
27
[ "b27" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
The number of putative intergenic insertions may change over time as better attachment site prediction algorithms are developed.
[ "27" ]
128
6,605
0
false
The number of putative intergenic insertions may change over time as better attachment site prediction algorithms are developed.
[]
The number of putative intergenic insertions may change over time as better attachment site prediction algorithms are developed.
true
true
true
true
true
1,083
1
DISCUSSION
1
27
[ "b27" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
It is also possible that the number of intragenic insertions is artificially too high since very small regions of nucleotide similarity can result in inaccurate target site prediction.
[ "27" ]
184
6,606
0
false
It is also possible that the number of intragenic insertions is artificially too high since very small regions of nucleotide similarity can result in inaccurate target site prediction.
[]
It is also possible that the number of intragenic insertions is artificially too high since very small regions of nucleotide similarity can result in inaccurate target site prediction.
true
true
true
true
true
1,083
1
DISCUSSION
1
27
[ "b27" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
The region of the tRNA gene that is targeted is very specific (the 3′ end of the gene in most instances) and can be quite large (up to 121 bp), which increases the confidence level of prediction over intragenic regions.
[ "27" ]
219
6,607
0
false
The region of the tRNA gene that is targeted is very specific (the 3′ end of the gene in most instances) and can be quite large (up to 121 bp), which increases the confidence level of prediction over intragenic regions.
[]
The region of the tRNA gene that is targeted is very specific (the 3′ end of the gene in most instances) and can be quite large, which increases the confidence level of prediction over intragenic regions.
true
true
true
true
true
1,083
1
DISCUSSION
1
27
[ "b27" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
The 5′ side of the D loop, the 3′ side of the anticodon loop and the anticodon were not previously known to be targeted by site-specific integrases (27).
[ "27" ]
153
6,608
1
false
The 5′ side of the D loop, the 3′ side of the anticodon loop and the anticodon were not previously known to be targeted by site-specific integrases.
[ "27" ]
The 5′ side of the D loop, the 3′ side of the anticodon loop and the anticodon were not previously known to be targeted by site-specific integrases.
true
true
true
true
true
1,083
1
DISCUSSION
1
27
[ "b27" ]
17,062,630
pmid-11448025|pmid-11792317|pmid-11842097
It remains to be determined whether these integrases actually function by inserting into the predicted locations in the tRNA genes.
[ "27" ]
131
6,609
0
false
It remains to be determined whether these integrases actually function by inserting into the predicted locations in the tRNA genes.
[]
It remains to be determined whether these integrases actually function by inserting into the predicted locations in the tRNA genes.
true
true
true
true
true
1,083
2
DISCUSSION
1
39
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
A new method for constructing phage trees was developed as a way to display the output of Phage_Finder and to determine whether such an approach might be useful as a way of grouping or classifying phages, prophages and predicted prophage regions from genomic sequences.
[ "39", "37", "9", "42", "45" ]
269
6,610
0
false
A new method for constructing phage trees was developed as a way to display the output of Phage_Finder and to determine whether such an approach might be useful as a way of grouping or classifying phages, prophages and predicted prophage regions from genomic sequences.
[]
A new method for constructing phage trees was developed as a way to display the output of Phage_Finder and to determine whether such an approach might be useful as a way of grouping or classifying phages, prophages and predicted prophage regions from genomic sequences.
true
true
true
true
true
1,084
2
DISCUSSION
1
39
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Instead of using protein alignments (39), the mean of the BSR was used to generate a PHYLIP distance matrix.
[ "39", "37", "9", "42", "45" ]
108
6,611
1
false
Instead of using protein alignments, the mean of the BSR was used to generate a PHYLIP distance matrix.
[ "39" ]
Instead of using protein alignments, the mean of the BSR was used to generate a PHYLIP distance matrix.
true
true
true
true
true
1,084
2
DISCUSSION
1
37
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Since the test tree, consisting of Campylobacter sequences rooted with Desulfovibrio vulgaris (Figure 3) was able to generate a tree that was consistent with the published concatenated protein tree (37), the results of such analysis are credible.
[ "39", "37", "9", "42", "45" ]
246
6,612
1
false
Since the test tree, consisting of Campylobacter sequences rooted with Desulfovibrio vulgaris (Figure 3) was able to generate a tree that was consistent with the published concatenated protein tree, the results of such analysis are credible.
[ "37" ]
Since the test tree, consisting of Campylobacter sequences rooted with Desulfovibrio vulgaris was able to generate a tree that was consistent with the published concatenated protein tree, the results of such analysis are credible.
true
true
true
true
true
1,084
2
DISCUSSION
1
39
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Further validity of this method came from the clustering of many known phages.
[ "39", "37", "9", "42", "45" ]
78
6,613
0
false
Further validity of this method came from the clustering of many known phages.
[]
Further validity of this method came from the clustering of many known phages.
true
true
true
true
true
1,084
2
DISCUSSION
1
39
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
One interesting result from Figure 4 was that RadMu did not cluster with other Mu-like phages.
[ "39", "37", "9", "42", "45" ]
94
6,614
0
false
One interesting result from Figure 4 was that RadMu did not cluster with other Mu-like phages.
[]
One interesting result from Figure 4 was that RadMu did not cluster with other Mu-like phages.
true
true
true
true
true
1,084
2
DISCUSSION
1
39
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Perhaps RadMu is defective and has changed considerably such that it doesn't match any other phage very well.
[ "39", "37", "9", "42", "45" ]
109
6,615
0
false
Perhaps RadMu is defective and has changed considerably such that it doesn't match any other phage very well.
[]
Perhaps RadMu is defective and has changed considerably such that it doesn't match any other phage very well.
true
true
true
true
true
1,084
2
DISCUSSION
1
39
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Alternatively, RadMu could represent a unique clade of Mu-like phage that has no other sequenced members.
[ "39", "37", "9", "42", "45" ]
105
6,616
0
false
Alternatively, RadMu could represent a unique clade of Mu-like phage that has no other sequenced members.
[]
Alternatively, RadMu could represent a unique clade of Mu-like phage that has no other sequenced members.
true
true
true
true
true
1,084
2
DISCUSSION
1
39
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Though this method is potentially very exciting because it is less computationally intensive than creating whole protein alignments and because there is no universal phylogenetic marker for studying phage evolution, caution must be exercised since many phages are mosaics of other phages (9,42,45).
[ "39", "37", "9", "42", "45" ]
298
6,617
0
false
Though this method is potentially very exciting because it is less computationally intensive than creating whole protein alignments and because there is no universal phylogenetic marker for studying phage evolution, caution must be exercised since many phages are mosaics of other phages.
[ "9,42,45" ]
Though this method is potentially very exciting because it is less computationally intensive than creating whole protein alignments and because there is no universal phylogenetic marker for studying phage evolution, caution must be exercised since many phages are mosaics of other phages.
true
true
true
true
true
1,084
2
DISCUSSION
1
39
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
However, this procedure does have utility for clustering related groups of phages and for classifying uncultured phages.
[ "39", "37", "9", "42", "45" ]
120
6,618
0
false
However, this procedure does have utility for clustering related groups of phages and for classifying uncultured phages.
[]
However, this procedure does have utility for clustering related groups of phages and for classifying uncultured phages.
true
true
true
true
true
1,084
2
DISCUSSION
1
39
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Furthermore, in a number of examples (Campylobacter, Listeria, Bacillus, Mycobacterium, Staphylococcus and Streptococcus phages and prophages), there is evidence to suggest coevolution of phages with host bacteria (Figure 4).
[ "39", "37", "9", "42", "45" ]
225
6,619
0
false
Furthermore, in a number of examples (Campylobacter, Listeria, Bacillus, Mycobacterium, Staphylococcus and Streptococcus phages and prophages), there is evidence to suggest coevolution of phages with host bacteria (Figure 4).
[]
Furthermore, in a number of examples (Campylobacter, Listeria, Bacillus, Mycobacterium, Staphylococcus and Streptococcus phages and prophages), there is evidence to suggest coevolution of phages with host bacteria (Figure 4).
true
true
true
true
true
1,084
2
DISCUSSION
1
39
[ "b39", "b37", "b9", "b42", "b45" ]
17,062,630
NA|pmid-9168627|pmid-12534463|pmid-12142423|pmid-15660156|pmid-11792317|pmid-12169615|pmid-10860721
Future versions might include either bonuses or penalties for synteny or the lack of synteny, which may resolve mosaic phages.
[ "39", "37", "9", "42", "45" ]
126
6,620
0
false
Future versions might include either bonuses or penalties for synteny or the lack of synteny, which may resolve mosaic phages.
[]
Future versions might include either bonuses or penalties for synteny or the lack of synteny, which may resolve mosaic phages.
true
true
true
true
true
1,084
3
DISCUSSION
0
null
null
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
Phage_Finder was initially developed to aid in the identification of prophage regions in complete bacterial genomes and to improve annotation of these genomes by associating some level of function to the many hypothetical and conserved hypothetical proteins that are encoded in bacterial genomes.
null
296
6,621
0
false
null
null
Phage_Finder was initially developed to aid in the identification of prophage regions in complete bacterial genomes and to improve annotation of these genomes by associating some level of function to the many hypothetical and conserved hypothetical proteins that are encoded in bacterial genomes.
true
true
true
true
true
1,085
3
DISCUSSION
0
null
null
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
It has been very successful in these goals and has even surfaced a few surprises.
null
81
6,622
0
false
null
null
It has been very successful in these goals and has even surfaced a few surprises.
true
true
true
true
true
1,085
3
DISCUSSION
0
null
null
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
For example, 10% of all proteins (20% of the hypothetical proteins) in the genome of Enterococcus faecalis V285 were within Phage_Finder-predicted putative prophage regions (D. E. Fouts, unpublished data).
null
205
6,623
0
false
null
null
For example, 10% of all proteins (20% of the hypothetical proteins) in the genome of Enterococcus faecalis V285 were within Phage_Finder-predicted putative prophage regions (D. E. Fouts, unpublished data).
true
true
true
true
true
1,085
3
DISCUSSION
0
null
null
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
Furthermore, even though E.coli O157:H7 Sakai had the greatest number of predicted prophage regions (13 under strict settings), Streptococcus pyogenes MGAS315, with six predicted prophage regions, had the highest percentage (13.6%) of its genome as prophage DNA.
null
262
6,624
0
false
null
null
Furthermore, even though E.coli O157:H7 Sakai had the greatest number of predicted prophage regions (13 under strict settings), Streptococcus pyogenes MGAS315, with six predicted prophage regions, had the highest percentage (13.6%) of its genome as prophage DNA.
true
true
true
true
true
1,085
3
DISCUSSION
0
null
null
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
Another surprise was how well Phage_Finder could identify genomic islands (pathogenecity islands, mec regions, integrated plasmids, which lead to the implementation of the ‘strict’ (-S) option.
null
193
6,625
0
false
null
null
Another surprise was how well Phage_Finder could identify genomic islands (pathogenecity islands, mec regions, integrated plasmids, which lead to the implementation of the ‘strict’ (-S) option.
true
true
true
true
true
1,085
3
DISCUSSION
0
null
null
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
This raises the question of whether phages evolved from these mobile elements or whether these mobile elements evolved from phages.
null
131
6,626
0
false
null
null
This raises the question of whether phages evolved from these mobile elements or whether these mobile elements evolved from phages.
true
true
true
true
true
1,085
3
DISCUSSION
0
null
null
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
Phage_Finder was run on all the complete archael genomes, but found no prophage regions under any setting.
null
106
6,627
0
false
null
null
Phage_Finder was run on all the complete archael genomes, but found no prophage regions under any setting.
true
true
true
true
true
1,085
3
DISCUSSION
0
null
null
17,062,630
pmid-9254694|pmid-2231712|pmid-9918945|pmid-2156132|pmid-10325427|pmid-2231712|pmid-9023104|pmid-14704338|pmid-12886937
It is not clear whether these archael genomes do not have integrated phages or whether the prophage regions are not detected because phages of this type are lacking from the BLAST-formated database.
null
198
6,628
0
false
null
null
It is not clear whether these archael genomes do not have integrated phages or whether the prophage regions are not detected because phages of this type are lacking from the BLAST-formated database.
true
true
true
true
true
1,085
4
DISCUSSION
0
null
null
17,062,630
null
The Phage_Finder pipeline will be a valuable tool for the scientific community and has been made publicly available ( or ).
null
123
6,629
0
false
null
null
The Phage_Finder pipeline will be a valuable tool for the scientific community and has been made publicly available ( or ).
true
true
true
true
true
1,086
4
DISCUSSION
0
null
null
17,062,630
null
Future plans are to integrate this pipleline into the existing infrastructure at TIGR and to make the results of Phage_Finder analysis publicly available.
null
154
6,630
0
false
null
null
Future plans are to integrate this pipleline into the existing infrastructure at TIGR and to make the results of Phage_Finder analysis publicly available.
true
true
true
true
true
1,086
4
DISCUSSION
0
null
null
17,062,630
null
It may also be possible to modify the program to identify integrated viruses in eukaryotic genomes, which would greatly facilitate the identification of retroviruses.
null
166
6,631
0
false
null
null
It may also be possible to modify the program to identify integrated viruses in eukaryotic genomes, which would greatly facilitate the identification of retroviruses.
true
true
true
true
true
1,086
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B2 B3 B4 B5", "B1", "B6" ]
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
Screening for genetic changes to unveil molecular attributes of human specimens is important for a variety of medical applications, including genotyping for inherited disorders, prediction of the pathologic behavior of malignancies, identification of cancer biomarkers and can affect treatment decisions for individual p...
[ "1–3", "2–5", "1", "6" ]
334
6,632
1
false
Screening for genetic changes to unveil molecular attributes of human specimens is important for a variety of medical applications, including genotyping for inherited disorders, prediction of the pathologic behavior of malignancies, identification of cancer biomarkers and can affect treatment decisions for individual p...
[ "1–3" ]
Screening for genetic changes to unveil molecular attributes of human specimens is important for a variety of medical applications, including genotyping for inherited disorders, prediction of the pathologic behavior of malignancies, identification of cancer biomarkers and can affect treatment decisions for individual p...
true
true
true
true
true
1,087
0
INTRODUCTION
1
2–5
[ "B1 B2 B3", "B2 B3 B4 B5", "B1", "B6" ]
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
For example, mutations in genes like EGFR can profoundly influence chemotherapeutic response in lung cancer (2–5) and the response is modulated by mutations in other genes of the same signaling pathway [e.g.
[ "1–3", "2–5", "1", "6" ]
207
6,633
1
false
For example, mutations in genes like EGFR can profoundly influence chemotherapeutic response in lung cancer and the response is modulated by mutations in other genes of the same signaling pathway [e.g.
[ "2–5" ]
For example, mutations in genes like EGFR can profoundly influence chemotherapeutic response in lung cancer and the response is modulated by mutations in other genes of the same signaling pathway [e.g.
true
true
true
true
true
1,087
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B2 B3 B4 B5", "B1", "B6" ]
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
K-ras, HER2, ErbB-3 (1,6)].
[ "1–3", "2–5", "1", "6" ]
27
6,634
0
false
K-ras, HER2, ErbB-3 ].
[ "1,6" ]
K-ras, HER2, ErbB-3 ].
true
true
true
true
true
1,087
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B2 B3 B4 B5", "B1", "B6" ]
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
Therefore there is a need for efficient and high-throughput mutation screening of multiple genes along identified signal transduction pathways in tumor samples.
[ "1–3", "2–5", "1", "6" ]
160
6,635
0
false
Therefore there is a need for efficient and high-throughput mutation screening of multiple genes along identified signal transduction pathways in tumor samples.
[]
Therefore there is a need for efficient and high-throughput mutation screening of multiple genes along identified signal transduction pathways in tumor samples.
true
true
true
true
true
1,087
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B2 B3 B4 B5", "B1", "B6" ]
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
Because a large portion of cancer-causing genetic changes remains unknown and can occur in numerous positions along tumor suppressor genes (e.g.
[ "1–3", "2–5", "1", "6" ]
144
6,636
0
false
Because a large portion of cancer-causing genetic changes remains unknown and can occur in numerous positions along tumor suppressor genes (e.g.
[]
Because a large portion of cancer-causing genetic changes remains unknown and can occur in numerous positions along tumor suppressor genes (e.g.
true
true
true
true
true
1,087
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B2 B3 B4 B5", "B1", "B6" ]
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
p53, ATM, PTEN)
[ "1–3", "2–5", "1", "6" ]
15
6,637
0
false
p53, ATM, PTEN)
[]
p53, ATM, PTEN)
false
true
false
true
false
1,087
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B2 B3 B4 B5", "B1", "B6" ]
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
mutation scanning rather than detection of specific mutations is frequently required for molecular cancer profiling.
[ "1–3", "2–5", "1", "6" ]
116
6,638
0
false
mutation scanning rather than detection of specific mutations is frequently required for molecular cancer profiling.
[]
mutation scanning rather than detection of specific mutations is frequently required for molecular cancer profiling.
false
true
true
true
false
1,087
1
INTRODUCTION
1
7–13
[ "B7 B8 B9 B10 B11 B12 B13", "B14", "B15", "B16", "B14", "B16 B17 B18 B19 B20", "B21 B22 B23 B24 B25", "B22", "B16", "B26", "B27", "B17", "B28", "B29 B30 B31 B32 B33 B34" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
Sequencing is often considered the gold standard for comprehensive mutation analysis.
[ "7–13", "14", "15", "16", "14", "16–20", "21–25", "22", "16", "26", "27", "17", "28", "29–34" ]
85
6,639
0
false
Sequencing is often considered the gold standard for comprehensive mutation analysis.
[]
Sequencing is often considered the gold standard for comprehensive mutation analysis.
true
true
true
true
true
1,088
1
INTRODUCTION
1
7–13
[ "B7 B8 B9 B10 B11 B12 B13", "B14", "B15", "B16", "B14", "B16 B17 B18 B19 B20", "B21 B22 B23 B24 B25", "B22", "B16", "B26", "B27", "B17", "B28", "B29 B30 B31 B32 B33 B34" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
Multi-capillary electrophoresis, re-sequencing arrays or pyrosequencing provide platforms for highly parallel genetic analysis (7–13).
[ "7–13", "14", "15", "16", "14", "16–20", "21–25", "22", "16", "26", "27", "17", "28", "29–34" ]
134
6,640
1
false
Multi-capillary electrophoresis, re-sequencing arrays or pyrosequencing provide platforms for highly parallel genetic analysis.
[ "7–13" ]
Multi-capillary electrophoresis, re-sequencing arrays or pyrosequencing provide platforms for highly parallel genetic analysis.
true
true
true
true
true
1,088
1
INTRODUCTION
1
7–13
[ "B7 B8 B9 B10 B11 B12 B13", "B14", "B15", "B16", "B14", "B16 B17 B18 B19 B20", "B21 B22 B23 B24 B25", "B22", "B16", "B26", "B27", "B17", "B28", "B29 B30 B31 B32 B33 B34" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
However, the expense associated with these techniques is currently high both for instrumentation and for running-costs.
[ "7–13", "14", "15", "16", "14", "16–20", "21–25", "22", "16", "26", "27", "17", "28", "29–34" ]
119
6,641
0
false
However, the expense associated with these techniques is currently high both for instrumentation and for running-costs.
[]
However, the expense associated with these techniques is currently high both for instrumentation and for running-costs.
true
true
true
true
true
1,088
1
INTRODUCTION
1
7–13
[ "B7 B8 B9 B10 B11 B12 B13", "B14", "B15", "B16", "B14", "B16 B17 B18 B19 B20", "B21 B22 B23 B24 B25", "B22", "B16", "B26", "B27", "B17", "B28", "B29 B30 B31 B32 B33 B34" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
Since somatic mutations for most genes are relatively rare events it can be inefficient to scan for mutations using expensive approaches that in several cases provide unnecessary data (14,15).
[ "7–13", "14", "15", "16", "14", "16–20", "21–25", "22", "16", "26", "27", "17", "28", "29–34" ]
192
6,642
0
false
Since somatic mutations for most genes are relatively rare events it can be inefficient to scan for mutations using expensive approaches that in several cases provide unnecessary data.
[ "14,15" ]
Since somatic mutations for most genes are relatively rare events it can be inefficient to scan for mutations using expensive approaches that in several cases provide unnecessary data.
true
true
true
true
true
1,088
1
INTRODUCTION
1
16
[ "B7 B8 B9 B10 B11 B12 B13", "B14", "B15", "B16", "B14", "B16 B17 B18 B19 B20", "B21 B22 B23 B24 B25", "B22", "B16", "B26", "B27", "B17", "B28", "B29 B30 B31 B32 B33 B34" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
Another issue with direct sequencing or re-sequencing arrays is the difficulty in detecting a small fraction of mutated alleles in the presence of a high excess normal alleles, which is frequently the case with clinical cancer samples (16).
[ "7–13", "14", "15", "16", "14", "16–20", "21–25", "22", "16", "26", "27", "17", "28", "29–34" ]
240
6,643
1
false
Another issue with direct sequencing or re-sequencing arrays is the difficulty in detecting a small fraction of mutated alleles in the presence of a high excess normal alleles, which is frequently the case with clinical cancer samples.
[ "16" ]
Another issue with direct sequencing or re-sequencing arrays is the difficulty in detecting a small fraction of mutated alleles in the presence of a high excess normal alleles, which is frequently the case with clinical cancer samples.
true
true
true
true
true
1,088
1
INTRODUCTION
1
7–13
[ "B7 B8 B9 B10 B11 B12 B13", "B14", "B15", "B16", "B14", "B16 B17 B18 B19 B20", "B21 B22 B23 B24 B25", "B22", "B16", "B26", "B27", "B17", "B28", "B29 B30 B31 B32 B33 B34" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
As a less expensive alternative, rapid pre-screening methods such as SSCP, DGGE, dHPLC, CCM, CDCE or HR-melting are widely utilized to identify DNA fragments that contain mutations prior to performing full sequencing (14,16–20).
[ "7–13", "14", "15", "16", "14", "16–20", "21–25", "22", "16", "26", "27", "17", "28", "29–34" ]
228
6,644
0
false
As a less expensive alternative, rapid pre-screening methods such as SSCP, DGGE, dHPLC, CCM, CDCE or HR-melting are widely utilized to identify DNA fragments that contain mutations prior to performing full sequencing.
[ "14,16–20" ]
As a less expensive alternative, rapid pre-screening methods such as SSCP, DGGE, dHPLC, CCM, CDCE or HR-melting are widely utilized to identify DNA fragments that contain mutations prior to performing full sequencing.
true
true
true
true
true
1,088
1
INTRODUCTION
1
16
[ "B7 B8 B9 B10 B11 B12 B13", "B14", "B15", "B16", "B14", "B16 B17 B18 B19 B20", "B21 B22 B23 B24 B25", "B22", "B16", "B26", "B27", "B17", "B28", "B29 B30 B31 B32 B33 B34" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
Enzymatic mutation detection based on mismatch scanning enzymes like MutY, TDG or T4 endonuclease VII for mutation pre-screening has also been employed (21–25), albeit with modest success since these enzymes cannot detect all possible mutations and deletions (22) and some of them have substantial activity on homoduplex...
[ "7–13", "14", "15", "16", "14", "16–20", "21–25", "22", "16", "26", "27", "17", "28", "29–34" ]
330
6,645
1
false
Enzymatic mutation detection based on mismatch scanning enzymes like MutY, TDG or T4 endonuclease VII for mutation pre-screening has also been employed, albeit with modest success since these enzymes cannot detect all possible mutations and deletions and some of them have substantial activity on homoduplex DNA.
[ "21–25", "22", "16" ]
Enzymatic mutation detection based on mismatch scanning enzymes like MutY, TDG or T4 endonuclease VII for mutation pre-screening has also been employed, albeit with modest success since these enzymes cannot detect all possible mutations and deletions and some of them have substantial activity on homoduplex DNA.
true
true
true
true
true
1,088
1
INTRODUCTION
1
7–13
[ "B7 B8 B9 B10 B11 B12 B13", "B14", "B15", "B16", "B14", "B16 B17 B18 B19 B20", "B21 B22 B23 B24 B25", "B22", "B16", "B26", "B27", "B17", "B28", "B29 B30 B31 B32 B33 B34" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
Recently an enzymatic mutation scanning method based on the Surveyor™ (CELI/II) nuclease (26,27) combined with dHPLC or gel electrophoresis detection was introduced that shows satisfactory selectivity and reliability (1% mutant to wild-type alleles is detectable) while it also identifies all base substitutions and smal...
[ "7–13", "14", "15", "16", "14", "16–20", "21–25", "22", "16", "26", "27", "17", "28", "29–34" ]
445
6,646
0
false
Recently an enzymatic mutation scanning method based on the Surveyor™ (CELI/II) nuclease combined with dHPLC or gel electrophoresis detection was introduced that shows satisfactory selectivity and reliability (1% mutant to wild-type alleles is detectable) while it also identifies all base substitutions and small deleti...
[ "26,27", "17,28", "TILLING method (29–34)" ]
Recently an enzymatic mutation scanning method based on the Surveyor™ (CELI/II) nuclease combined with dHPLC or gel electrophoresis detection was introduced that shows satisfactory selectivity and reliability while it also identifies all base substitutions and small deletions that are important to cancer or to biotechn...
true
true
true
true
true
1,088
1
INTRODUCTION
1
7–13
[ "B7 B8 B9 B10 B11 B12 B13", "B14", "B15", "B16", "B14", "B16 B17 B18 B19 B20", "B21 B22 B23 B24 B25", "B22", "B16", "B26", "B27", "B17", "B28", "B29 B30 B31 B32 B33 B34" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
While reliable, the use of dHPLC for examining Surveyor™-generated DNA fragments is a slow endpoint detection method restricted to examining a single DNA fragment at a time and the resulting DNA fragments cannot be sequenced.
[ "7–13", "14", "15", "16", "14", "16–20", "21–25", "22", "16", "26", "27", "17", "28", "29–34" ]
225
6,647
0
false
While reliable, the use of dHPLC for examining Surveyor™-generated DNA fragments is a slow endpoint detection method restricted to examining a single DNA fragment at a time and the resulting DNA fragments cannot be sequenced.
[]
While reliable, the use of dHPLC for examining Surveyor™-generated DNA fragments is a slow endpoint detection method restricted to examining a single DNA fragment at a time and the resulting DNA fragments cannot be sequenced.
true
true
true
true
true
1,088
1
INTRODUCTION
1
7–13
[ "B7 B8 B9 B10 B11 B12 B13", "B14", "B15", "B16", "B14", "B16 B17 B18 B19 B20", "B21 B22 B23 B24 B25", "B22", "B16", "B26", "B27", "B17", "B28", "B29 B30 B31 B32 B33 B34" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
This limits analysis of cancer specimens when numerous samples or genetic regions need to be screened.
[ "7–13", "14", "15", "16", "14", "16–20", "21–25", "22", "16", "26", "27", "17", "28", "29–34" ]
102
6,648
0
false
This limits analysis of cancer specimens when numerous samples or genetic regions need to be screened.
[]
This limits analysis of cancer specimens when numerous samples or genetic regions need to be screened.
true
true
true
true
true
1,088
2
INTRODUCTION
0
null
null
17,545,195
null
We introduce a new approach that enables Surveyor™ to scan for mutations over one or several PCR products simultaneously and selectively amplify and isolate the mutation-containing DNA fragment(s) via linker-mediated PCR.
null
221
6,649
0
false
null
null
We introduce a new approach that enables Surveyor™ to scan for mutations over one or several PCR products simultaneously and selectively amplify and isolate the mutation-containing DNA fragment(s) via linker-mediated PCR.
true
true
true
true
true
1,089
2
INTRODUCTION
0
null
null
17,545,195
null
By selectively amplifying mutation-containing DNA from wild-type fragments, the present approach de-couples enzymatic mutation scanning from the endpoint detection step.
null
169
6,650
0
false
null
null
By selectively amplifying mutation-containing DNA from wild-type fragments, the present approach de-couples enzymatic mutation scanning from the endpoint detection step.
true
true
true
true
true
1,089
2
INTRODUCTION
0
null
null
17,545,195
null
As a result, following enzymatic action on mismatches any chosen DNA detection method (real-time PCR, gel/capillary electrophoresis, microarray-based detection) can potentially be used to identify the mutated DNA fragments in a simplex or multiplex fashion.
null
257
6,651
0
false
null
null
As a result, following enzymatic action on mismatches any chosen DNA detection method (real-time PCR, gel/capillary electrophoresis, microarray-based detection) can potentially be used to identify the mutated DNA fragments in a simplex or multiplex fashion.
true
true
true
true
true
1,089
2
INTRODUCTION
0
null
null
17,545,195
null
Here we utilize real-time PCR coupled with melting curve analysis (Surveyor™-mediated Real Time Melting, s-RT-MELT) to validate the new technology.
null
147
6,652
0
false
null
null
Here we utilize real-time PCR coupled with melting curve analysis (Surveyor™-mediated Real Time Melting, s-RT-MELT) to validate the new technology.
true
true
true
true
true
1,089
2
INTRODUCTION
0
null
null
17,545,195
null
We demonstrate that this approach increases the mutation scanning throughput by 1–2 orders of magnitude when several (>100) samples are to be pre-scanned for mutations, enables mutation scanning over several PCR fragments simultaneously and mutation-positive samples can be directly sequenced when somatic mutations are ...
null
399
6,653
0
false
null
null
We demonstrate that this approach increases the mutation scanning throughput by 1–2 orders of magnitude when several (>100) samples are to be pre-scanned for mutations, enables mutation scanning over several PCR fragments simultaneously and mutation-positive samples can be directly sequenced when somatic mutations are ...
true
true
true
true
true
1,089
0
DISCUSSION
0
null
null
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
The intrinsic potential of enzymatic mutation scanning for parallel identification of mutations can, in principle, be very high since the enzyme operates on numerous distinct mismatch-containing sequences on a molecule-to-molecule basis thus providing highly parallel mutation scanning.
null
286
6,654
0
false
null
null
The intrinsic potential of enzymatic mutation scanning for parallel identification of mutations can, in principle, be very high since the enzyme operates on numerous distinct mismatch-containing sequences on a molecule-to-molecule basis thus providing highly parallel mutation scanning.
true
true
true
true
true
1,090
0
DISCUSSION
0
null
null
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
However, in the past the selectivity of the enzymes used and the endpoint detection method has limited the realization of this potential.
null
137
6,655
0
false
null
null
However, in the past the selectivity of the enzymes used and the endpoint detection method has limited the realization of this potential.
true
true
true
true
true
1,090
0
DISCUSSION
0
null
null
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
Here we enabled Surveyor™, an endonuclease that recognizes selectively mismatches formed by mutations and small deletions following ‘cross-hybridized sequence’ formation, to generate mutation-specific DNA fragments that are amplified and screened via differential melting curve analysis.
null
287
6,656
0
false
null
null
Here we enabled Surveyor™, an endonuclease that recognizes selectively mismatches formed by mutations and small deletions following ‘cross-hybridized sequence’ formation, to generate mutation-specific DNA fragments that are amplified and screened via differential melting curve analysis.
true
true
true
true
true
1,090
0
DISCUSSION
0
null
null
17,545,195
pmid-16728632|pmid-15118125|pmid-15728811|pmid-15118125|pmid-15728811|pmid-15118073|pmid-15329413|pmid-16728632|pmid-16231326
The replacement of size-separation methods (capillary/gel electrophoresis, dHPLC) by real-time PCR technology as the endpoint detection platforms and the ability to scan more than one sequences in parallel result in a highly increased throughput for s-RT-MELT while retaining the ability to detect diverse mutations at l...
null
330
6,657
0
false
null
null
The replacement of size-separation methods (capillary/gel electrophoresis, dHPLC) by real-time PCR technology as the endpoint detection platforms and the ability to scan more than one sequences in parallel result in a highly increased throughput for s-RT-MELT while retaining the ability to detect diverse mutations at l...
true
true
true
true
true
1,090
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
Cel I/II endonucleases have also been known to have exonuclease activity on 5′ DNA-ends (26,27).
[ "26", "27", "46", "47" ]
96
6,658
0
false
Cel I/II endonucleases have also been known to have exonuclease activity on 5′ DNA-ends.
[ "26,27" ]
Cel I/II endonucleases have also been known to have exonuclease activity on 5′ DNA-ends.
true
true
true
true
true
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
For this reason, s-RT-MELT was designed to attach an oligonucleotide linker to the 3′-DNA ends via terminal transferase (TdT) instead of using the 5′-DNA ends.
[ "26", "27", "46", "47" ]
159
6,659
0
false
For this reason, s-RT-MELT was designed to attach an oligonucleotide linker to the 3′-DNA ends via terminal transferase (TdT) instead of using the 5′-DNA ends.
[]
For this reason, s-RT-MELT was designed to attach an oligonucleotide linker to the 3′-DNA ends via terminal transferase (TdT) instead of using the 5′-DNA ends.
true
true
true
true
true
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
The exonuclease activity also tends to degrade the attached 5′-GC-clamps in s-RT-MELT, thereby eliminating their influence in reducing amplification of un-digested fragments.
[ "26", "27", "46", "47" ]
174
6,660
0
false
The exonuclease activity also tends to degrade the attached 5′-GC-clamps in s-RT-MELT, thereby eliminating their influence in reducing amplification of un-digested fragments.
[]
The exonuclease activity also tends to degrade the attached 5′-GC-clamps in s-RT-MELT, thereby eliminating their influence in reducing amplification of un-digested fragments.
true
true
true
true
true
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
We found that if exposure of DNA ‘cross-hybridized sequences’ to Surveyor™ is limited to 15–20 min, the substantial degradation of 5′-GC-clamps is avoided.
[ "26", "27", "46", "47" ]
155
6,661
0
false
We found that if exposure of DNA ‘cross-hybridized sequences’ to Surveyor™ is limited to 15–20 min, the substantial degradation of 5′-GC-clamps is avoided.
[]
We found that if exposure of DNA ‘cross-hybridized sequences’ to Surveyor™ is limited to 15–20 min, the substantial degradation of 5′-GC-clamps is avoided.
true
true
true
true
true
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
For multiplexing mutation detection using several PCR products simultaneously, the size of the GC-clamp on each PCR amplicon may need to be individually adjusted to ensure that mutations along all sequence positions of the PCR products included in the mixture can be screened at a single real-time PCR temperature and th...
[ "26", "27", "46", "47" ]
359
6,662
0
false
For multiplexing mutation detection using several PCR products simultaneously, the size of the GC-clamp on each PCR amplicon may need to be individually adjusted to ensure that mutations along all sequence positions of the PCR products included in the mixture can be screened at a single real-time PCR temperature and th...
[]
For multiplexing mutation detection using several PCR products simultaneously, the size of the GC-clamp on each PCR amplicon may need to be individually adjusted to ensure that mutations along all sequence positions of the PCR products included in the mixture can be screened at a single real-time PCR temperature and th...
true
true
true
true
true
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
The calculational tools developed in this work can be used to guide the individual design of GC-clamps.
[ "26", "27", "46", "47" ]
103
6,663
0
false
The calculational tools developed in this work can be used to guide the individual design of GC-clamps.
[]
The calculational tools developed in this work can be used to guide the individual design of GC-clamps.
true
true
true
true
true
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
s-RT-MELT detects heterozygous SNPs as well as mutations.
[ "26", "27", "46", "47" ]
57
6,664
0
false
s-RT-MELT detects heterozygous SNPs as well as mutations.
[]
s-RT-MELT detects heterozygous SNPs as well as mutations.
false
true
true
true
false
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
As with other mutation pre-screening techniques, the presence of a SNP concurrently with a mutation might be difficult to identify without performing sequencing.
[ "26", "27", "46", "47" ]
161
6,665
0
false
As with other mutation pre-screening techniques, the presence of a SNP concurrently with a mutation might be difficult to identify without performing sequencing.
[]
As with other mutation pre-screening techniques, the presence of a SNP concurrently with a mutation might be difficult to identify without performing sequencing.
true
true
true
true
true
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
Because SNPs occur at fixed positions, melting peaks originating from SNPs have a reproducible pattern and melting temperatures (46,47) thus in many cases they should be distinguishable from mutations.
[ "26", "27", "46", "47" ]
201
6,666
0
false
Because SNPs occur at fixed positions, melting peaks originating from SNPs have a reproducible pattern and melting temperatures thus in many cases they should be distinguishable from mutations.
[ "46,47" ]
Because SNPs occur at fixed positions, melting peaks originating from SNPs have a reproducible pattern and melting temperatures thus in many cases they should be distinguishable from mutations.
true
true
true
true
true
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
Finally, it is noteworthy that s-RT-MELT is a general methodology that may also be applied to isolate mutations using mismatch-cutting enzymes other than Surveyor™ when enzymes with satisfactory properties for mutation detection become available.
[ "26", "27", "46", "47" ]
246
6,667
0
false
Finally, it is noteworthy that s-RT-MELT is a general methodology that may also be applied to isolate mutations using mismatch-cutting enzymes other than Surveyor™ when enzymes with satisfactory properties for mutation detection become available.
[]
Finally, it is noteworthy that s-RT-MELT is a general methodology that may also be applied to isolate mutations using mismatch-cutting enzymes other than Surveyor™ when enzymes with satisfactory properties for mutation detection become available.
true
true
true
true
true
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
Detection platforms other than real-time PCR/melting (e.g.
[ "26", "27", "46", "47" ]
58
6,668
0
false
Detection platforms other than real-time PCR/melting (e.g.
[]
Detection platforms other than real-time PCR/melting (e.g.
true
true
true
true
true
1,091
1
DISCUSSION
1
26
[ "B26", "B27", "B46", "B47" ]
17,545,195
NA|pmid-11217341|pmid-9915500|pmid-14993206|pmid-16165119|pmid-16799556|pmid-16056220|pmid-11722288|pmid-16140923|pmid-9216447|pmid-11722288|pmid-9216447|pmid-15948293|pmid-3260032|pmid-11242964|pmid-16191501|pmid-9973620|pmid-12124995|pmid-15108270|pmid-7816853|pmid-8995763|pmid-12124995|pmid-9216447|pmid-10736152|pmi...
DNA microarray-based) may also be envisioned following enzymatic mutation selection.
[ "26", "27", "46", "47" ]
84
6,669
0
false
DNA microarray-based) may also be envisioned following enzymatic mutation selection.
[]
DNA microarray-based) may also be envisioned following enzymatic mutation selection.
true
true
true
true
true
1,091
2
DISCUSSION
0
null
null
17,545,195
null
In summary, we developed a new method for rapid mutation scanning, s-RT-MELT that utilizes the Cel I/II (Surveyor™) and terminal deoxy-nucleotide transferase (TdT) enzymes to isolate and amplify mutation-containing DNA fragments without the requirement of DNA size-dependent techniques.
null
286
6,670
0
false
null
null
In summary, we developed a new method for rapid mutation scanning, s-RT-MELT that utilizes the Cel I/II (Surveyor™) and terminal deoxy-nucleotide transferase (TdT) enzymes to isolate and amplify mutation-containing DNA fragments without the requirement of DNA size-dependent techniques.
true
true
true
true
true
1,092
2
DISCUSSION
0
null
null
17,545,195
null
Besides enabling highly increased throughput, multiplexed mutation screening and direct sequencing of the identified mutant DNA fragments, s-RT-MELT also retains the advantages of the Surveyor endonuclease over alternative pre-screening methods, such as reliability and identification of genetic alterations present at l...
null
355
6,671
0
false
null
null
Besides enabling highly increased throughput, multiplexed mutation screening and direct sequencing of the identified mutant DNA fragments, s-RT-MELT also retains the advantages of the Surveyor endonuclease over alternative pre-screening methods, such as reliability and identification of genetic alterations present at l...
true
true
true
true
true
1,092
2
DISCUSSION
0
null
null
17,545,195
null
s-RT-MELT provides a significant advancement in unknown mutation scanning in cancer research and diagnostics as well as for general medical, biological and biotechnology applications.
null
183
6,672
0
false
null
null
s-RT-MELT provides a significant advancement in unknown mutation scanning in cancer research and diagnostics as well as for general medical, biological and biotechnology applications.
false
true
true
true
false
1,092
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,616
pmid-10381871|pmid-10508729|pmid-10830951|pmid-16292353
One lesson of comparative genomics has been that numerous intricate and interdependent processes underlie organismal evolution.
[ "1", "2", "3" ]
127
6,673
0
false
One lesson of comparative genomics has been that numerous intricate and interdependent processes underlie organismal evolution.
[]
One lesson of comparative genomics has been that numerous intricate and interdependent processes underlie organismal evolution.
true
true
true
true
true
1,093
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,616
pmid-10381871|pmid-10508729|pmid-10830951|pmid-16292353
Even attempts to obtain an unambiguous picture of bacterial evolutionary relationships—organisms which reproduce in the absence of genetic exchange—have often been confounded with the emergence of the data that contradict accepted beliefs.
[ "1", "2", "3" ]
239
6,674
0
false
Even attempts to obtain an unambiguous picture of bacterial evolutionary relationships—organisms which reproduce in the absence of genetic exchange—have often been confounded with the emergence of the data that contradict accepted beliefs.
[]
Even attempts to obtain an unambiguous picture of bacterial evolutionary relationships—organisms which reproduce in the absence of genetic exchange—have often been confounded with the emergence of the data that contradict accepted beliefs.
true
true
true
true
true
1,093
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,616
pmid-10381871|pmid-10508729|pmid-10830951|pmid-16292353
For example, while bacterial phylogenies have historically used the highly conserved sequences of the small subunit ribosomal RNA, more complete genome sequence data has documented significant levels of gene transfer between the distantly related organisms, a strongly confounding influence on the elucidation of taxonom...
[ "1", "2", "3" ]
341
6,675
1
false
For example, while bacterial phylogenies have historically used the highly conserved sequences of the small subunit ribosomal RNA, more complete genome sequence data has documented significant levels of gene transfer between the distantly related organisms, a strongly confounding influence on the elucidation of taxonom...
[ "1" ]
For example, while bacterial phylogenies have historically used the highly conserved sequences of the small subunit ribosomal RNA, more complete genome sequence data has documented significant levels of gene transfer between the distantly related organisms, a strongly confounding influence on the elucidation of taxonom...
true
true
true
true
true
1,093
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,591,616
pmid-10381871|pmid-10508729|pmid-10830951|pmid-16292353
Beyond obfuscating the tree form of life, lateral gene transfer (LGT) mobilizes ecologically important genes among taxa, making it a potent force in the diversification and speciation of prokaryotes (2,3).
[ "1", "2", "3" ]
205
6,676
0
false
Beyond obfuscating the tree form of life, lateral gene transfer (LGT) mobilizes ecologically important genes among taxa, making it a potent force in the diversification and speciation of prokaryotes.
[ "2,3" ]
Beyond obfuscating the tree form of life, lateral gene transfer (LGT) mobilizes ecologically important genes among taxa, making it a potent force in the diversification and speciation of prokaryotes.
true
true
true
true
true
1,093
1
INTRODUCTION
1
4
[ "B4", "B5", "B6" ]
17,591,616
pmid-11470360|pmid-12975657|pmid-15913459
Change in gene inventory is a historical process.
[ "4", "5", "6" ]
49
6,677
0
false
Change in gene inventory is a historical process.
[]
Change in gene inventory is a historical process.
true
true
true
true
true
1,094
1
INTRODUCTION
1
4
[ "B4", "B5", "B6" ]
17,591,616
pmid-11470360|pmid-12975657|pmid-15913459
In the absence of experimental means to determine the evolutionary history of a gene, several complementary methods have been developed to infer the occurrence of gene transfer events, categorized as phylogenetic incongruency tests and parametric methods.
[ "4", "5", "6" ]
255
6,678
0
false
In the absence of experimental means to determine the evolutionary history of a gene, several complementary methods have been developed to infer the occurrence of gene transfer events, categorized as phylogenetic incongruency tests and parametric methods.
[]
In the absence of experimental means to determine the evolutionary history of a gene, several complementary methods have been developed to infer the occurrence of gene transfer events, categorized as phylogenetic incongruency tests and parametric methods.
true
true
true
true
true
1,094
1
INTRODUCTION
1
4
[ "B4", "B5", "B6" ]
17,591,616
pmid-11470360|pmid-12975657|pmid-15913459
The former identifies single gene topologies that deviate significantly from consensus relationships; aberrant phylogenies are considered to be the most reliable indicator of ancestral gene transfer events.
[ "4", "5", "6" ]
206
6,679
0
false
The former identifies single gene topologies that deviate significantly from consensus relationships; aberrant phylogenies are considered to be the most reliable indicator of ancestral gene transfer events.
[]
The former identifies single gene topologies that deviate significantly from consensus relationships; aberrant phylogenies are considered to be the most reliable indicator of ancestral gene transfer events.
true
true
true
true
true
1,094
1
INTRODUCTION
1
4
[ "B4", "B5", "B6" ]
17,591,616
pmid-11470360|pmid-12975657|pmid-15913459
Caveats for their use include biased mutation rates, improper clade selection, gene loss, segregation of paralogs and long branch length attraction (4).
[ "4", "5", "6" ]
152
6,680
1
false
Caveats for their use include biased mutation rates, improper clade selection, gene loss, segregation of paralogs and long branch length attraction.
[ "4" ]
Caveats for their use include biased mutation rates, improper clade selection, gene loss, segregation of paralogs and long branch length attraction.
true
true
true
true
true
1,094
1
INTRODUCTION
1
4
[ "B4", "B5", "B6" ]
17,591,616
pmid-11470360|pmid-12975657|pmid-15913459
More importantly, the success of phylogenetic methods depends entirely on the breadth and depth of the sequence database, which is especially evident in the inability to use these approaches to identify orphan genes of foreign origin.
[ "4", "5", "6" ]
234
6,681
0
false
More importantly, the success of phylogenetic methods depends entirely on the breadth and depth of the sequence database, which is especially evident in the inability to use these approaches to identify orphan genes of foreign origin.
[]
More importantly, the success of phylogenetic methods depends entirely on the breadth and depth of the sequence database, which is especially evident in the inability to use these approaches to identify orphan genes of foreign origin.
true
true
true
true
true
1,094
1
INTRODUCTION
1
4
[ "B4", "B5", "B6" ]
17,591,616
pmid-11470360|pmid-12975657|pmid-15913459
Lastly, phylogenetic studies may yield ambiguous results.
[ "4", "5", "6" ]
57
6,682
0
false
Lastly, phylogenetic studies may yield ambiguous results.
[]
Lastly, phylogenetic studies may yield ambiguous results.
true
true
true
true
true
1,094
1
INTRODUCTION
1
5
[ "B4", "B5", "B6" ]
17,591,616
pmid-11470360|pmid-12975657|pmid-15913459
For example, a recent survey of 13 species of γ-proteobacteria concluded that few LGT events took place among them, since organismal relationships inferred from the sequences of most genes failed to reject the consensus topology (5); however, it was later reported that these same data failed to reject any topology, not...
[ "4", "5", "6" ]
477
6,683
1
false
For example, a recent survey of 13 species of γ-proteobacteria concluded that few LGT events took place among them, since organismal relationships inferred from the sequences of most genes failed to reject the consensus topology ; however, it was later reported that these same data failed to reject any topology, not on...
[ "5", "6" ]
For example, a recent survey of 13 species of γ-proteobacteria concluded that few LGT events took place among them, since organismal relationships inferred from the sequences of most genes failed to reject the consensus topology ; however, it was later reported that these same data failed to reject any topology, not on...
true
true
true
true
true
1,094
2
INTRODUCTION
1
7
[ "B7", "B8", "B4", "B9" ]
17,591,616
pmid-9089078|pmid-9689094|pmid-11470360|pmid-16292353
In contrast, parametric approaches are based on the hypothesis that sequence features are similar within a genome but differ significantly between genomes.
[ "7", "8", "4", "9" ]
155
6,684
0
false
In contrast, parametric approaches are based on the hypothesis that sequence features are similar within a genome but differ significantly between genomes.
[]
In contrast, parametric approaches are based on the hypothesis that sequence features are similar within a genome but differ significantly between genomes.
true
true
true
true
true
1,095
2
INTRODUCTION
1
7
[ "B7", "B8", "B4", "B9" ]
17,591,616
pmid-9089078|pmid-9689094|pmid-11470360|pmid-16292353
Genes which share a common set of features —that is, typical genes—are classified as native.
[ "7", "8", "4", "9" ]
92
6,685
0
false
Genes which share a common set of features —that is, typical genes—are classified as native.
[]
Genes which share a common set of features —that is, typical genes—are classified as native.
true
true
true
true
true
1,095
2
INTRODUCTION
1
7
[ "B7", "B8", "B4", "B9" ]
17,591,616
pmid-9089078|pmid-9689094|pmid-11470360|pmid-16292353
In contrast, putatively foreign genes have atypical features inconsistent with the patterns reflected by the bulk of the genome; the features of these genes are posited to reflect the mutational proclivities of their donor organisms.
[ "7", "8", "4", "9" ]
233
6,686
0
false
In contrast, putatively foreign genes have atypical features inconsistent with the patterns reflected by the bulk of the genome; the features of these genes are posited to reflect the mutational proclivities of their donor organisms.
[]
In contrast, putatively foreign genes have atypical features inconsistent with the patterns reflected by the bulk of the genome; the features of these genes are posited to reflect the mutational proclivities of their donor organisms.
true
true
true
true
true
1,095
2
INTRODUCTION
1
7
[ "B7", "B8", "B4", "B9" ]
17,591,616
pmid-9089078|pmid-9689094|pmid-11470360|pmid-16292353
While ancient gene transfer events would be difficult to detect as their atypical features ameliorate (7,8), genes of recent foreign origin are of special interest to microbiologists due to their role in recent changes in their ecological niche and/or metabolic repertoire.
[ "7", "8", "4", "9" ]
273
6,687
0
false
While ancient gene transfer events would be difficult to detect as their atypical features ameliorate, genes of recent foreign origin are of special interest to microbiologists due to their role in recent changes in their ecological niche and/or metabolic repertoire.
[ "7,8" ]
While ancient gene transfer events would be difficult to detect as their atypical features ameliorate, genes of recent foreign origin are of special interest to microbiologists due to their role in recent changes in their ecological niche and/or metabolic repertoire.
true
true
true
true
true
1,095
2
INTRODUCTION
1
4
[ "B7", "B8", "B4", "B9" ]
17,591,616
pmid-9089078|pmid-9689094|pmid-11470360|pmid-16292353
However, the sets of foreign genes detected by parametric approaches often differ significantly (4); this may result from the different metrics being utilized, or different thresholds used to discriminate between ‘typical’ and ‘atypical’ genes.
[ "7", "8", "4", "9" ]
244
6,688
1
false
However, the sets of foreign genes detected by parametric approaches often differ significantly ; this may result from the different metrics being utilized, or different thresholds used to discriminate between ‘typical’ and ‘atypical’ genes.
[ "4" ]
However, the sets of foreign genes detected by parametric approaches often differ significantly ; this may result from the different metrics being utilized, or different thresholds used to discriminate between ‘typical’ and ‘atypical’ genes.
true
true
true
true
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INTRODUCTION
1
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[ "B7", "B8", "B4", "B9" ]
17,591,616
pmid-9089078|pmid-9689094|pmid-11470360|pmid-16292353
Such conflicts between methods have not been easy to resolve; until recently, the efficacy of parametric methods had been difficult to assess due to the lack of benchmark protocols (9).
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Such conflicts between methods have not been easy to resolve; until recently, the efficacy of parametric methods had been difficult to assess due to the lack of benchmark protocols.
[ "9" ]
Such conflicts between methods have not been easy to resolve; until recently, the efficacy of parametric methods had been difficult to assess due to the lack of benchmark protocols.
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INTRODUCTION
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[ "B10", "B9", "B11" ]
17,591,616
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Yet these caveats are somewhat minor compared to an intrinsic weakness shared by nearly all parametric methods.
[ "10", "9", "11" ]
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Yet these caveats are somewhat minor compared to an intrinsic weakness shared by nearly all parametric methods.
[]
Yet these caveats are somewhat minor compared to an intrinsic weakness shared by nearly all parametric methods.
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1,096
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INTRODUCTION
1
10
[ "B10", "B9", "B11" ]
17,591,616
pmid-1762151|pmid-16292353|pmid-16176988|pmid-9847079
Rather than falling into totally discrete groups corresponding to typical and atypical genes, compositional features of genes lie along a continuum (Figure 1A).
[ "10", "9", "11" ]
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Rather than falling into totally discrete groups corresponding to typical and atypical genes, compositional features of genes lie along a continuum (Figure 1A).
[]
Rather than falling into totally discrete groups corresponding to typical and atypical genes, compositional features of genes lie along a continuum.
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1,096
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INTRODUCTION
1
10
[ "B10", "B9", "B11" ]
17,591,616
pmid-1762151|pmid-16292353|pmid-16176988|pmid-9847079
That is, there is no easily defined threshold beyond which atypical genes are clearly of foreign origin.
[ "10", "9", "11" ]
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That is, there is no easily defined threshold beyond which atypical genes are clearly of foreign origin.
[]
That is, there is no easily defined threshold beyond which atypical genes are clearly of foreign origin.
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true
true
true
true
1,096
3
INTRODUCTION
1
10
[ "B10", "B9", "B11" ]
17,591,616
pmid-1762151|pmid-16292353|pmid-16176988|pmid-9847079
Native genes may also be strongly atypical; for example, highly expressed genes have codon usage bias patterns that distinguish them from the majority of chromosomal genes (10).
[ "10", "9", "11" ]
177
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Native genes may also be strongly atypical; for example, highly expressed genes have codon usage bias patterns that distinguish them from the majority of chromosomal genes.
[ "10" ]
Native genes may also be strongly atypical; for example, highly expressed genes have codon usage bias patterns that distinguish them from the majority of chromosomal genes.
true
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1,096
3
INTRODUCTION
1
9
[ "B10", "B9", "B11" ]
17,591,616
pmid-1762151|pmid-16292353|pmid-16176988|pmid-9847079
As a result, arbitrary thresholds must be employed for declaring atypical genes to be of likely foreign origin, where choice of threshold balances Type I and Type II errors (9).
[ "10", "9", "11" ]
177
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As a result, arbitrary thresholds must be employed for declaring atypical genes to be of likely foreign origin, where choice of threshold balances Type I and Type II errors.
[ "9" ]
As a result, arbitrary thresholds must be employed for declaring atypical genes to be of likely foreign origin, where choice of threshold balances Type I and Type II errors.
true
true
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true
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1,096
3
INTRODUCTION
1
10
[ "B10", "B9", "B11" ]
17,591,616
pmid-1762151|pmid-16292353|pmid-16176988|pmid-9847079
Conservative thresholds lead to rare misclassification of native genes as foreign, at the expense of more falsely declared native genes.
[ "10", "9", "11" ]
136
6,695
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Conservative thresholds lead to rare misclassification of native genes as foreign, at the expense of more falsely declared native genes.
[]
Conservative thresholds lead to rare misclassification of native genes as foreign, at the expense of more falsely declared native genes.
true
true
true
true
true
1,096
3
INTRODUCTION
1
10
[ "B10", "B9", "B11" ]
17,591,616
pmid-1762151|pmid-16292353|pmid-16176988|pmid-9847079
Liberal thresholds detect more foreign genes, but also incur more false predictions (i.e.
[ "10", "9", "11" ]
89
6,696
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Liberal thresholds detect more foreign genes, but also incur more false predictions (i.e.
[]
Liberal thresholds detect more foreign genes, but also incur more false predictions (i.e.
true
true
true
true
true
1,096
3
INTRODUCTION
1
10
[ "B10", "B9", "B11" ]
17,591,616
pmid-1762151|pmid-16292353|pmid-16176988|pmid-9847079
native genes misclassified as foreign).
[ "10", "9", "11" ]
39
6,697
0
false
native genes misclassified as foreign).
[]
native genes misclassified as foreign).
false
true
true
true
false
1,096
3
INTRODUCTION
1
10
[ "B10", "B9", "B11" ]
17,591,616
pmid-1762151|pmid-16292353|pmid-16176988|pmid-9847079
Advances in the efficacy of parametric methods critically depend upon a decoupling of Type I and Type II errors, so that genes that lie in the twilight zone (the somewhat atypical native genes or weakly atypical foreign genes) may be robustly classified as either native or foreign.
[ "10", "9", "11" ]
282
6,698
0
false
Advances in the efficacy of parametric methods critically depend upon a decoupling of Type I and Type II errors, so that genes that lie in the twilight zone (the somewhat atypical native genes or weakly atypical foreign genes) may be robustly classified as either native or foreign.
[]
Advances in the efficacy of parametric methods critically depend upon a decoupling of Type I and Type II errors, so that genes that lie in the twilight zone (the somewhat atypical native genes or weakly atypical foreign genes) may be robustly classified as either native or foreign.
true
true
true
true
true
1,096
3
INTRODUCTION
1
10
[ "B10", "B9", "B11" ]
17,591,616
pmid-1762151|pmid-16292353|pmid-16176988|pmid-9847079
To accomplish this goal, we use two features of gene transfer in bacterial genomes.
[ "10", "9", "11" ]
83
6,699
0
false
To accomplish this goal, we use two features of gene transfer in bacterial genomes.
[]
To accomplish this goal, we use two features of gene transfer in bacterial genomes.
true
true
true
true
true
1,096