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Nephele: genotyping via complete composition vectors and MapReduce

Overview of attention for article published in Source Code for Biology and Medicine, August 2011
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3 X users

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Title
Nephele: genotyping via complete composition vectors and MapReduce
Published in
Source Code for Biology and Medicine, August 2011
DOI 10.1186/1751-0473-6-13
Pubmed ID
Authors

Marc E Colosimo, Matthew W Peterson, Scott Mardis, Lynette Hirschman

Abstract

Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences.

X Demographics

X Demographics

The data shown below were collected from the profiles of 3 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 41 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 4 10%
Indonesia 1 2%
France 1 2%
Unknown 35 85%

Demographic breakdown

Readers by professional status Count As %
Researcher 10 24%
Student > Ph. D. Student 8 20%
Other 6 15%
Lecturer 3 7%
Student > Postgraduate 3 7%
Other 8 20%
Unknown 3 7%
Readers by discipline Count As %
Computer Science 16 39%
Agricultural and Biological Sciences 15 37%
Biochemistry, Genetics and Molecular Biology 3 7%
Medicine and Dentistry 2 5%
Social Sciences 1 2%
Other 1 2%
Unknown 3 7%
Attention Score in Context

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 23 August 2011.
All research outputs
#14,136,253
of 22,651,245 outputs
Outputs from Source Code for Biology and Medicine
#75
of 127 outputs
Outputs of similar age
#81,771
of 123,300 outputs
Outputs of similar age from Source Code for Biology and Medicine
#1
of 2 outputs
Altmetric has tracked 22,651,245 research outputs across all sources so far. This one is in the 35th percentile – i.e., 35% of other outputs scored the same or lower than it.
So far Altmetric has tracked 127 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 8.0. This one is in the 36th percentile – i.e., 36% 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 123,300 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 31st percentile – i.e., 31% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 2 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