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The exceptional genomic word symmetry along DNA sequences

Overview of attention for article published in BMC Bioinformatics, February 2016
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (84th percentile)
  • High Attention Score compared to outputs of the same age and source (80th percentile)

Mentioned by

blogs
1 blog
twitter
6 tweeters

Citations

dimensions_citation
5 Dimensions

Readers on

mendeley
24 Mendeley
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Title
The exceptional genomic word symmetry along DNA sequences
Published in
BMC Bioinformatics, February 2016
DOI 10.1186/s12859-016-0905-0
Pubmed ID
Authors

Vera Afreixo, João M. O. S. Rodrigues, Carlos A. C. Bastos, Raquel M. Silva

Abstract

The second Chargaff's parity rule and its extensions are recognized as universal phenomena in DNA sequences. However, parity of the frequencies of reverse complementary oligonucleotides could be a mere consequence of the single nucleotide parity rule, if nucleotide independence is assumed. Exceptional symmetry (symmetry beyond that expected under an independent nucleotide assumption) was proposed previously as a meaningful measure of the extension of the second parity rule to oligonucleotides. The global exceptional symmetry was detected in long and short genomes. To explore the exceptional genomic word symmetry along the genome sequences, we propose a sliding window method to extract the values of exceptional symmetry (for all words or by word groups). We compare the exceptional symmetry effect size distribution in all human chromosomes against control scenarios (positive and negative controls), testing the differences and performing a residual analysis. We explore local exceptional symmetry in equivalent composition word groups, and find that the behaviour of the local exceptional symmetry depends on the word group. We conclude that the exceptional symmetry is a local phenomenon in genome sequences, with distinct characteristics along the sequence of each chromosome. The local exceptional symmetry along the genomic sequences shows outlying segments, and those segments have high biological annotation density.

Twitter Demographics

The data shown below were collected from the profiles of 6 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 24 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 4%
Finland 1 4%
Unknown 22 92%

Demographic breakdown

Readers by professional status Count As %
Researcher 5 21%
Professor > Associate Professor 4 17%
Student > Ph. D. Student 4 17%
Other 3 13%
Professor 3 13%
Other 5 21%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 6 25%
Computer Science 4 17%
Engineering 4 17%
Agricultural and Biological Sciences 4 17%
Immunology and Microbiology 2 8%
Other 4 17%

Attention Score in Context

This research output has an Altmetric Attention Score of 9. 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 02 March 2016.
All research outputs
#1,613,662
of 12,378,687 outputs
Outputs from BMC Bioinformatics
#647
of 4,543 outputs
Outputs of similar age
#52,663
of 339,489 outputs
Outputs of similar age from BMC Bioinformatics
#27
of 136 outputs
Altmetric has tracked 12,378,687 research outputs across all sources so far. Compared to these this one has done well and is in the 86th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 4,543 research outputs from this source. They receive a mean Attention Score of 4.9. This one has done well, scoring higher than 85% 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 339,489 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 84% of its contemporaries.
We're also able to compare this research output to 136 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 80% of its contemporaries.