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FRESCo: finding regions of excess synonymous constraint in diverse viruses

Overview of attention for article published in Genome Biology, February 2015
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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 (91st percentile)
  • Above-average Attention Score compared to outputs of the same age and source (57th percentile)

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2 blogs
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12 X users
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2 Facebook pages
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1 Google+ user

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35 Dimensions

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67 Mendeley
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Title
FRESCo: finding regions of excess synonymous constraint in diverse viruses
Published in
Genome Biology, February 2015
DOI 10.1186/s13059-015-0603-7
Pubmed ID
Authors

Rachel S Sealfon, Michael F Lin, Irwin Jungreis, Maxim Y Wolf, Manolis Kellis, Pardis C Sabeti

Abstract

The increasing availability of sequence data for many viruses provides power to detect regions under unusual evolutionary constraint at a high resolution. One approach leverages the synonymous substitution rate as a signature to pinpoint genic regions encoding overlapping or embedded functional elements. Protein-coding regions in viral genomes often contain overlapping RNA structural elements, reading frames, regulatory elements, microRNAs, and packaging signals. Synonymous substitutions in these regions would be selectively disfavored and thus these regions are characterized by excess synonymous constraint. Codon choice can also modulate transcriptional efficiency, translational accuracy, and protein folding. We developed a phylogenetic codon model-based framework, FRESCo, designed to find regions of excess synonymous constraint in short, deep alignments, such as individual viral genes across many sequenced isolates. We demonstrated the high specificity of our approach on simulated data and applied our framework to the protein-coding regions of approximately 30 distinct species of viruses with diverse genome architectures. FRESCo recovers known multifunctional regions in well-characterized viruses such as hepatitis B virus, poliovirus, and West Nile virus, often at a single-codon resolution, and predicts many novel functional elements overlapping viral genes, including in Lassa and Ebola viruses. In a number of viruses, the synonymously constrained regions that we identified also display conserved, stable predicted RNA structures, including putative novel elements in multiple viral species.

X Demographics

X Demographics

The data shown below were collected from the profiles of 12 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 67 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 67 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 20 30%
Student > Master 10 15%
Researcher 10 15%
Student > Postgraduate 5 7%
Other 5 7%
Other 10 15%
Unknown 7 10%
Readers by discipline Count As %
Agricultural and Biological Sciences 19 28%
Biochemistry, Genetics and Molecular Biology 17 25%
Medicine and Dentistry 7 10%
Nursing and Health Professions 4 6%
Computer Science 4 6%
Other 7 10%
Unknown 9 13%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 19. 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 17 May 2021.
All research outputs
#1,905,078
of 25,371,288 outputs
Outputs from Genome Biology
#1,586
of 4,467 outputs
Outputs of similar age
#23,343
of 269,050 outputs
Outputs of similar age from Genome Biology
#30
of 71 outputs
Altmetric has tracked 25,371,288 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 92nd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 4,467 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.6. This one has gotten more attention than average, scoring higher than 64% 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 269,050 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 91% of its contemporaries.
We're also able to compare this research output to 71 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.