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Visualization of consensus genome structure without using a reference genome

Overview of attention for article published in BMC Genomics, March 2017
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3 tweeters

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3 Dimensions

Readers on

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28 Mendeley
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Title
Visualization of consensus genome structure without using a reference genome
Published in
BMC Genomics, March 2017
DOI 10.1186/s12864-017-3499-7
Pubmed ID
Authors

Ipputa Tada, Yasuhiro Tanizawa, Masanori Arita

Abstract

Standard graphical tools for whole genome comparison require a reference genome. However, any reference is also subject to annotation biases and rearrangements, and may not serve as the standard except for those of extensively studied model species. To fully exploit the rapidly accumulating sequence data from the recent sequencing technologies, genome comparison without any reference has been anticipated. We introduce a circular genome visualizer to compare complete genomes of closely related species. This tool visualizes the position of orthologous gene clusters rather than actual sequences or their features, thereby achieving the comparative view without using a single reference genome. The essential information is the matrix of orthologous gene clusters whose positions (not sequences) are color-coded in circular graphics. As a demonstration, comparison of 14 Lactobacillus paracasei strains and one L. casei strain revealed not only large-scale rearrangements but also genomic islands that are strain-specific. Comparison of 73 Helicobacter pylori strains confirmed their genetic consistency and also revealed the three general patterns of large-scale genome inversions. From the ample sequence information in the GenBank/ENA/DDBJ repository, we can reconstruct a genomic consensus for particular species. By visualizing multiple strains at a glance, we can identify conserved as well as strain-specific regions in multiply sequenced genomes. Positional consistency for orthologous genes provides information orthogonal to major sequence features such as the GC content or sequence similarity of marker genes. The positional comparison is therefore useful for identifying large-scale genome rearrangements or gene transfers.

Twitter Demographics

The data shown below were collected from the profiles of 3 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 28 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Thailand 1 4%
Unknown 27 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 9 32%
Researcher 5 18%
Student > Bachelor 3 11%
Student > Doctoral Student 2 7%
Professor 2 7%
Other 3 11%
Unknown 4 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 9 32%
Biochemistry, Genetics and Molecular Biology 5 18%
Immunology and Microbiology 2 7%
Computer Science 1 4%
Chemical Engineering 1 4%
Other 2 7%
Unknown 8 29%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 10 December 2020.
All research outputs
#11,845,630
of 19,680,162 outputs
Outputs from BMC Genomics
#4,847
of 9,835 outputs
Outputs of similar age
#144,301
of 280,046 outputs
Outputs of similar age from BMC Genomics
#9
of 21 outputs
Altmetric has tracked 19,680,162 research outputs across all sources so far. This one is in the 38th percentile – i.e., 38% of other outputs scored the same or lower than it.
So far Altmetric has tracked 9,835 research outputs from this source. They receive a mean Attention Score of 4.5. This one is in the 47th percentile – i.e., 47% of its peers scored the same or lower than it.
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 280,046 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 46th percentile – i.e., 46% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 21 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 57% of its contemporaries.