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The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure

Overview of attention for article published in BMC Bioinformatics, May 2018
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  • Above-average Attention Score compared to outputs of the same age and source (54th percentile)

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1 tweeter

Citations

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Title
The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure
Published in
BMC Bioinformatics, May 2018
DOI 10.1186/s12859-018-2161-y
Pubmed ID
Authors

Maxwell Shapiro, Stephen Meier, Thomas MacCarthy

Abstract

Activation induced deaminase (AID) and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) are deaminases that mutate C to U on single-stranded DNA (ssDNA). AID is expressed primarily in germinal center B-cells, where it facilitates affinity maturation and class-switch recombination. APOBEC3 are a family of anti-viral proteins that act as part of the intrinsic immune response. In both cases, there are particular sequence motifs, also known as "mutation motifs", to which these deaminases prefer to bind and mutate. We present a program, the cytidine deaminase under-representation reporter (CDUR) designed to statistically determine whether a given sequence has an under/over-representation of these mutation motifs. CDUR shows consitency with other studies of mutation motifs, as we show by analyzing sequences from the adeno-associated virus 2 (AAV2) and human papillomavirus (HPV). Using various shuffling mechanisms to generate different null model distributions, we can tailor CDUR to correct for metrics such as GC-content, dinucleotide frequency, and codon bias.

Twitter Demographics

The data shown below were collected from the profile of 1 tweeter 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 20 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 20 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 6 30%
Researcher 4 20%
Student > Postgraduate 3 15%
Student > Master 3 15%
Student > Bachelor 2 10%
Other 1 5%
Unknown 1 5%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 8 40%
Agricultural and Biological Sciences 5 25%
Medicine and Dentistry 2 10%
Immunology and Microbiology 2 10%
Mathematics 1 5%
Other 0 0%
Unknown 2 10%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 03 May 2018.
All research outputs
#10,284,097
of 12,886,920 outputs
Outputs from BMC Bioinformatics
#3,985
of 4,806 outputs
Outputs of similar age
#201,483
of 269,061 outputs
Outputs of similar age from BMC Bioinformatics
#10
of 22 outputs
Altmetric has tracked 12,886,920 research outputs across all sources so far. This one is in the 11th percentile – i.e., 11% of other outputs scored the same or lower than it.
So far Altmetric has tracked 4,806 research outputs from this source. They receive a mean Attention Score of 4.9. This one is in the 7th percentile – i.e., 7% 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 269,061 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 13th percentile – i.e., 13% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 22 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 54% of its contemporaries.