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Coordinates and intervals in graph-based reference genomes

Overview of attention for article published in BMC Bioinformatics, May 2017
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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 (89th percentile)
  • High Attention Score compared to outputs of the same age and source (93rd percentile)

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33 X users
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1 patent
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1 Facebook page

Citations

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22 Dimensions

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60 Mendeley
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Title
Coordinates and intervals in graph-based reference genomes
Published in
BMC Bioinformatics, May 2017
DOI 10.1186/s12859-017-1678-9
Pubmed ID
Authors

Knut D. Rand, Ivar Grytten, Alexander J. Nederbragt, Geir O. Storvik, Ingrid K. Glad, Geir K. Sandve

Abstract

It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph-based reference genomes. We formalize offset-based coordinate systems on graph-based reference genomes and introduce methods for representing intervals on these reference structures. We show the advantage of our methods by representing genes on a graph-based representation of the newest assembly of the human genome (GRCh38) and its alternative loci for regions that are highly variable. More complex reference genomes, containing alternative loci, require methods to represent genomic data on these structures. Our proposed notation for genomic intervals makes it possible to fully utilize the alternative loci of the GRCh38 assembly and potential future graph-based reference genomes. We have made a Python package for representing such intervals on offset-based coordinate systems, available at https://github.com/uio-cels/offsetbasedgraph . An interactive web-tool using this Python package to visualize genes on a graph created from GRCh38 is available at https://github.com/uio-cels/genomicgraphcoords .

X Demographics

X Demographics

The data shown below were collected from the profiles of 33 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 60 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 3%
Japan 1 2%
France 1 2%
Unknown 56 93%

Demographic breakdown

Readers by professional status Count As %
Researcher 15 25%
Student > Ph. D. Student 13 22%
Student > Master 12 20%
Student > Bachelor 6 10%
Professor 2 3%
Other 7 12%
Unknown 5 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 21 35%
Biochemistry, Genetics and Molecular Biology 16 27%
Computer Science 10 17%
Engineering 3 5%
Medicine and Dentistry 3 5%
Other 1 2%
Unknown 6 10%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 21. 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 08 April 2021.
All research outputs
#1,590,536
of 23,577,761 outputs
Outputs from BMC Bioinformatics
#304
of 7,418 outputs
Outputs of similar age
#32,316
of 314,872 outputs
Outputs of similar age from BMC Bioinformatics
#7
of 105 outputs
Altmetric has tracked 23,577,761 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 7,418 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 particularly well, scoring higher than 95% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 314,872 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 89% of its contemporaries.
We're also able to compare this research output to 105 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 93% of its contemporaries.