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Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data

Overview of attention for article published in BMC Bioinformatics, January 2015
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (84th percentile)

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14 tweeters

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61 Mendeley
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Title
Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data
Published in
BMC Bioinformatics, January 2015
DOI 10.1186/s12859-014-0449-0
Pubmed ID
Authors

Sterling Sawaya, James Boocock, Michael A Black, Neil J Gemmell

Abstract

BackgroundPausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences sequencer reads can be related to DNA sequences. The Pacific Biosciences sequencer uses optics to view a polymerase and its interaction with a single DNA molecule in real-time, offering a unique way to detect potential alternative DNA structures.ResultsWe have developed a new way to examine polymerase kinetics data and relate it to the DNA sequence by using a wavelet transform of read information from the sequencer. We use this method to examine how polymerase kinetics are related to nucleotide base composition. We then examine tandem repeat sequences known for their ability to form different DNA structures: (CGG)n and (CG)n repeats which can, respectively, form G-quadruplex DNA and Z-DNA. We find pausing around the (CGG)n repeat that may indicate the presence of G-quadruplexes in some of the sequencer reads. The (CG)n repeat does not appear to cause polymerase pausing, but its kinetics signature nevertheless suggests the possibility that alternative nucleotide conformations may sometimes be present.ConclusionWe discuss the implications of using our method to discover DNA sequences capable of forming alternative structures. The analyses presented here can be reproduced on any Pacific Biosciences kinetics data for any DNA pattern of interest using an R package that we have made publicly available.

Twitter Demographics

The data shown below were collected from the profiles of 14 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 61 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 3%
Norway 1 2%
Unknown 58 95%

Demographic breakdown

Readers by professional status Count As %
Student > Master 13 21%
Student > Ph. D. Student 12 20%
Researcher 10 16%
Student > Bachelor 5 8%
Professor > Associate Professor 5 8%
Other 10 16%
Unknown 6 10%
Readers by discipline Count As %
Agricultural and Biological Sciences 24 39%
Biochemistry, Genetics and Molecular Biology 15 25%
Computer Science 6 10%
Medicine and Dentistry 3 5%
Chemistry 3 5%
Other 4 7%
Unknown 6 10%

Attention Score in Context

This research output has an Altmetric Attention Score of 9. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 21 September 2019.
All research outputs
#3,332,665
of 20,419,783 outputs
Outputs from BMC Bioinformatics
#1,356
of 6,775 outputs
Outputs of similar age
#49,944
of 315,829 outputs
Outputs of similar age from BMC Bioinformatics
#1
of 1 outputs
Altmetric has tracked 20,419,783 research outputs across all sources so far. Compared to these this one has done well and is in the 83rd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 6,775 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one has done well, scoring higher than 80% of its peers.
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We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them