ProkAtlas is a bioinformatic database and analysis pipeline that infer the habitat environment of prokaryotes from their 16S rRNA gene sequences.
Although prokaryotic species are distributed worldwide, these species cannot adapt to every environment. Each species can proliferate in a specific combination of environmental settings to a different extent, leading to the current biodiversity of the microbial ecology. Thus, habitat information well represents the ecological traits of prokaryotes.
By using ProkAtlas, you can answer questions such as the following:
ProkAtlas is also applicable to community-scale data (such as 16S rRNA/rDNA amplicon sequences): prokaryotic community composition data can be presented as the "composition of habitats".
ProkAtlas searches its environmental 16S rRNA database and reveals which environments the species bearing the query 16S rRNA(s) can be found.
ProkAtlas Online Toolkit will be temporarily unavailable because of the scheduled blackout. Possible down time is scheduled as follows:
Greenwich Mean Time (GMT): Sep 23 (Fri), 2022 from 12:00 GMT - Sep 24 (Sat) 18:00 GMT
New York, USA: Sep 23 (Fri), 2022 from 7:00 EST - Sep 24 (Sat) 13:00 EST
Los Angeles, USA: Sep 23 (Fri), 2022 from 4:00 PDT - Sep 24 (Sat) 10:00 PDT
Beijing, China: Sep 23 (Fri), 2022 from 20:00 CST - Sep 24 (Sat), 17:00 CST
Tokyo, Japan: Sep 23 (Fri), 2022 from 21:00 JST - Sep 24 (Sat), 18:00 JST
We provide web user interface (ProkAtlas Online) here. We also provide databases and scripts for calculating habitat preference scores.
To obtain the habitat preference information of individual prokaryotic species, you just need their intact 16S ribosomal RNA/DNA sequence(s). If you like to calculate habitat preference scores (i.e. habitat compositions) of prokaryotic communities, also prepare a tab-spaced OTU table along with 16S rRNA/rDNA sequences (i.e. OTU representative sequences).
Source code for calculating microbial habitat preference scores (This script is written in python and requires pandas)
If you used ProkAtlas in your study, please cite the following paper:
