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MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics

Overview of attention for article published in BMC Bioinformatics, 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 (83rd percentile)

Mentioned by

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16 tweeters
facebook
3 Facebook pages

Citations

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6 Dimensions

Readers on

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103 Mendeley
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Title
MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics
Published in
BMC Bioinformatics, February 2015
DOI 10.1186/s12859-015-0501-8
Pubmed ID
Authors

Sandeep K Kushwaha, Lokeshwaran Manoharan, Tejashwari Meerupati, Katarina Hedlund, Dag Ahrén

Abstract

Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families. In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 300,000 probes that match more than 400,000 publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/ . MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.

Twitter Demographics

The data shown below were collected from the profiles of 16 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 103 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 3%
Brazil 3 3%
Singapore 1 <1%
Canada 1 <1%
Sweden 1 <1%
Belgium 1 <1%
China 1 <1%
Estonia 1 <1%
France 1 <1%
Other 0 0%
Unknown 90 87%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 32 31%
Researcher 31 30%
Student > Master 10 10%
Other 8 8%
Student > Bachelor 7 7%
Other 12 12%
Unknown 3 3%
Readers by discipline Count As %
Agricultural and Biological Sciences 57 55%
Biochemistry, Genetics and Molecular Biology 18 17%
Computer Science 7 7%
Immunology and Microbiology 5 5%
Environmental Science 2 2%
Other 3 3%
Unknown 11 11%

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 23 June 2017.
All research outputs
#1,911,686
of 13,426,363 outputs
Outputs from BMC Bioinformatics
#782
of 4,990 outputs
Outputs of similar age
#35,800
of 214,725 outputs
Outputs of similar age from BMC Bioinformatics
#1
of 1 outputs
Altmetric has tracked 13,426,363 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 4,990 research outputs from this source. They receive a mean Attention Score of 4.9. This one has done well, scoring higher than 84% 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 214,725 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 83% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them