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Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology

Overview of attention for article published in PeerJ, October 2014
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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)
  • Above-average Attention Score compared to outputs of the same age and source (61st percentile)

Mentioned by

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14 X users
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1 peer review site
facebook
2 Facebook pages

Citations

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7 Dimensions

Readers on

mendeley
27 Mendeley
citeulike
2 CiteULike
Title
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology
Published in
PeerJ, October 2014
DOI 10.7717/peerj.607
Pubmed ID
Authors

Lucas D. Wittwer, Ivana Piližota, Adrian M. Altenhoff, Christophe Dessimoz

Abstract

Orthology inference and other sequence analyses across multiple genomes typically start by performing exhaustive pairwise sequence comparisons, a process referred to as "all-against-all". As this process scales quadratically in terms of the number of sequences analysed, this step can become a bottleneck, thus limiting the number of genomes that can be simultaneously analysed. Here, we explored ways of speeding-up the all-against-all step while maintaining its sensitivity. By exploiting the transitivity of homology and, crucially, ensuring that homology is defined in terms of consistent protein subsequences, our proof-of-concept resulted in a 4× speedup while recovering >99.6% of all homologs identified by the full all-against-all procedure on empirical sequences sets. In comparison, state-of-the-art k-mer approaches are orders of magnitude faster but only recover 3-14% of all homologous pairs. We also outline ideas to further improve the speed and recall of the new approach. An open source implementation is provided as part of the OMA standalone software at http://omabrowser.org/standalone.

X Demographics

X Demographics

The data shown below were collected from the profiles of 14 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 27 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 2 7%
Germany 1 4%
Portugal 1 4%
United States 1 4%
Poland 1 4%
Unknown 21 78%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 6 22%
Student > Master 6 22%
Researcher 5 19%
Student > Bachelor 3 11%
Professor 2 7%
Other 2 7%
Unknown 3 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 13 48%
Biochemistry, Genetics and Molecular Biology 6 22%
Computer Science 3 11%
Immunology and Microbiology 1 4%
Physics and Astronomy 1 4%
Other 0 0%
Unknown 3 11%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 10. 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 21 November 2014.
All research outputs
#3,621,892
of 25,373,627 outputs
Outputs from PeerJ
#3,645
of 15,147 outputs
Outputs of similar age
#39,772
of 267,625 outputs
Outputs of similar age from PeerJ
#57
of 147 outputs
Altmetric has tracked 25,373,627 research outputs across all sources so far. Compared to these this one has done well and is in the 85th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 15,147 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 17.1. This one has done well, scoring higher than 75% 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 267,625 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 147 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 61% of its contemporaries.