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Online Interactive Microbial Classification and Geospatial Distributional Analysis Using BioAtlas

  • Jesper Lund
  • Qihua Tan
  • Jan Baumbach
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1807)

Abstract

In recent decades, the accumulation of data on 16s ribosomal RNA genes has yielded free and public databases such as SILVA, GreenGenes, The Ribosomal Database Project, and IMG, handling massive amounts of raw data and meta information. 16s rRNA gene contains hypervariable regions with great classification power. As a result, numerous classification tools have emerged including state-of-the-art tools such as Mothur, Qiime, and the 16s classifier. However, there is a gap between the sequence databases, the taxonomy profiling tools and available meta information such as geo/body-location information. Here, we present BioAtlas, and interactive web tool for searching, exploring, and analyzing prokaryotic distributions by integration of various resources of metagenomics databases. In the following section we show how to use BioAtlas to (1) search and explore prokaryote occurrences across the geospatial map of the world, (2) investigate and hunt for occurrences across generic user-generated surface-specific maps, with an example map of a human female, with data from Bouslimani et al., and (3) classify a user-given sequences dataset through our online platform for visual exploration of the spatial abundances of the identified microbes.

Key words

Taxonomic classification 16s gene Ribosomal RNA Distributional analysis Microbiology Online tool Maps Data mining Integration Metadata 

Notes

Acknowledgements

JBL is grateful for financial support from his VILLUM Young Investigator Grant. Funding for open access charge: VILLUM Young Investigator Grant of Jan Baumbach (Young Investigator Grant nr. 13154).

JBL is grateful for financial support from his Velux Foundation research grant (Research grant nr. 000121540), supporting his Ph.D. project.

Conflict of Interest Statement

None declared.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Jesper Lund
    • 1
  • Qihua Tan
    • 2
  • Jan Baumbach
    • 3
    • 4
  1. 1.Epidemiology and Biostatistics, Department of Public HealthUniversity of Southern DenmarkOdenseDenmark
  2. 2.Epidemiology and Biostatistics, Department of Public HealthUniversity of Southern DenmarkOdenseDenmark
  3. 3.University of Southern DenmarkOdenseDenmark
  4. 4.Technical University of MunichMunichGermany

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