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Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

Overview of attention for article published in BMC Genomics, August 2016
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (59th percentile)
  • Above-average Attention Score compared to outputs of the same age and source (60th percentile)

Mentioned by

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7 tweeters

Citations

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64 Dimensions

Readers on

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136 Mendeley
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Title
Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies
Published in
BMC Genomics, August 2016
DOI 10.1186/s12864-016-3018-2
Pubmed ID
Authors

Bryan D. Merrill, Andy T. Ward, Julianne H. Grose, Sandra Hope

Abstract

Phage genome analysis is a rapidly growing field. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator databases. We further report genomic analysis techniques to determine phage packaging strategies and identification of the physical ends of phage genomes. The original Phamerator code can be successfully modified and custom databases can be generated using the instructions we provide. Results of genome map comparisons within a custom database reveal obstacles in performing the comparisons if a published genome has an incorrect complementarity or an incorrect location of the first base of the genome, which are common issues in GenBank-downloaded sequence files. To address these issues, we review phage packaging strategies and provide results that demonstrate identification of the genome start location and orientation using raw sequencing data and software programs such as PAUSE and Consed to establish the location of the physical ends of the genome. These results include determination of exact direct terminal repeats (DTRs) or cohesive ends, or whether phages may use a headful packaging strategy. Phylogenetic analysis using ClustalO and phamily circles in Phamerator demonstrate that the large terminase gene can be used to identify the phage packaging strategy and thereby aide in identifying the physical ends of the genome. Using available online code, the Phamerator program can be customized and utilized to generate databases with individually selected genomes. These databases can then provide fruitful information in the comparative analysis of phages. Researchers can identify packaging strategies and physical ends of phage genomes using raw data from high-throughput sequencing in conjunction with phylogenetic analyses of large terminase proteins and the use of custom Phamerator databases. We promote publication of phage genomes in an orientation consistent with the physical structure of the phage chromosome and provide guidance for determining this structure.

Twitter Demographics

The data shown below were collected from the profiles of 7 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 136 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 136 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 28 21%
Student > Bachelor 23 17%
Researcher 22 16%
Student > Master 9 7%
Professor > Associate Professor 8 6%
Other 19 14%
Unknown 27 20%
Readers by discipline Count As %
Agricultural and Biological Sciences 38 28%
Biochemistry, Genetics and Molecular Biology 27 20%
Immunology and Microbiology 17 13%
Environmental Science 3 2%
Medicine and Dentistry 3 2%
Other 14 10%
Unknown 34 25%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 27 August 2016.
All research outputs
#3,485,534
of 8,286,032 outputs
Outputs from BMC Genomics
#2,448
of 5,854 outputs
Outputs of similar age
#98,695
of 252,882 outputs
Outputs of similar age from BMC Genomics
#100
of 273 outputs
Altmetric has tracked 8,286,032 research outputs across all sources so far. This one has received more attention than most of these and is in the 57th percentile.
So far Altmetric has tracked 5,854 research outputs from this source. They receive a mean Attention Score of 4.2. This one has gotten more attention than average, scoring higher than 55% 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 252,882 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 59% of its contemporaries.
We're also able to compare this research output to 273 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 60% of its contemporaries.