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CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences

Overview of attention for article published in BMC Bioinformatics, December 2017
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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 (86th percentile)
  • High Attention Score compared to outputs of the same age and source (89th percentile)

Mentioned by

blogs
1 blog
twitter
10 tweeters

Citations

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53 Dimensions

Readers on

mendeley
91 Mendeley
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Title
CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences
Published in
BMC Bioinformatics, December 2017
DOI 10.1186/s12859-017-1952-x
Pubmed ID
Authors

Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol, Gregory Bonito

Abstract

One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies. While bioinformatics pipelines that cluster reads into OTUs have received much attention in the literature, less attention has been given to the taxonomic classification of these sequences, upon which biological inference is dependent. Here we compare how three common fungal OTU taxonomic assignment tools (RDP Classifier, UTAX, and SINTAX) handle ITS fungal sequence data. The classification power, defined as the proportion of assigned OTUs at a given taxonomic rank, varied among the classifiers. Classifiers were generally consistent (assignment of the same taxonomy to a given OTU) across datasets and ranks; a small number of OTUs were assigned unique classifications across programs. We developed CONSTAX (CONSensus TAXonomy), a Python tool that compares taxonomic classifications of the three programs and merges them into an improved consensus taxonomy. This tool also produces summary classification outputs that are useful for downstream analyses. Our results demonstrate that independent taxonomy assignment tools classify unique members of the fungal community, and greater classification power is realized by generating consensus taxonomy of available classifiers with CONSTAX.

Twitter Demographics

The data shown below were collected from the profiles of 10 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 91 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 91 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 29 32%
Student > Ph. D. Student 12 13%
Student > Master 8 9%
Student > Bachelor 7 8%
Student > Doctoral Student 5 5%
Other 10 11%
Unknown 20 22%
Readers by discipline Count As %
Agricultural and Biological Sciences 28 31%
Biochemistry, Genetics and Molecular Biology 12 13%
Environmental Science 9 10%
Engineering 4 4%
Immunology and Microbiology 3 3%
Other 10 11%
Unknown 25 27%

Attention Score in Context

This research output has an Altmetric Attention Score of 13. 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 January 2019.
All research outputs
#2,150,479
of 20,927,597 outputs
Outputs from BMC Bioinformatics
#700
of 6,851 outputs
Outputs of similar age
#61,234
of 441,089 outputs
Outputs of similar age from BMC Bioinformatics
#46
of 441 outputs
Altmetric has tracked 20,927,597 research outputs across all sources so far. Compared to these this one has done well and is in the 89th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 6,851 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one has done well, scoring higher than 89% 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 441,089 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 86% of its contemporaries.
We're also able to compare this research output to 441 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 89% of its contemporaries.