Online interactive microbial classification and geospatial distributional analysis using BioAtlas

Jesper Lund, Qihua Tan, Jan Baumbach

Publikation: Kapitel i bog/rapport/konference-proceedingKapitel i bogForskningpeer review

Abstrakt

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.
OriginalsprogEngelsk
TitelData Mining for Systems Biology : Methods and Protocols
RedaktørerHiroshi Mamitsuka
Vol/bind1807
UdgivelsesstedNew York
ForlagHumana Press
Publikationsdato2018
Sider21-35
Kapitel3
ISBN (Trykt)9781493985609
ISBN (Elektronisk)978143985616
DOI
StatusUdgivet - 2018
NavnMethods in Molecular Biology
Vol/bind1807
ISSN1064-3745

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