janzrimec / plastic_degrading_microbiome

Plastic-degrading potential across the global microbiome correlates with recent pollution trends

Link to paper: 10.1128/mBio.02155-21

Figure. Depiction of plastic-degrading enzymes across the global microbiome obtained by constructing HMM models of known plastic-degrading enzymes and querying them across metagenomic sequencing datasets. We observed 11,906 enzyme hits in the ocean and 18,119 in the soil datasets, with the potential to degrade 10 and 9 different plastic types, respectively.

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This repository contains scripts to reproduce the analysis and figures. The data is available at , extract the archive to a folder named 'data'.

Dependencies are provided in the conda environment.yml file in the 'docs' folder.

plastic_degrading_microbiome's Issues

question: protein sequences of plastic-degrading enzymes?

@JanZrimec nice work!

Here's a question regarding the obtained ~30k plastic-degrading enzymes detected from ocean (11,906) and soil (18,119) in this study. Where to download the protein sequences of these enzymes?

I've gone through this repo and the associated Zenodo site, but failed in finding the sequences. Could you please point me to the right place, which probably was missed by me.

Best, Hao

CD-HIT to HMMs

Greetings!

I am trying to employ a similar strategy to yours for obtaining HMMs, but have found it difficult to obtain from CD-HIT an output that will be accepted by hmmbuild to generate HMMs.

Searching through this repo I could not find the commands to replicate going from a FASTA of protein sequences to a final HMM, have I missed those commands or are they not available here? If so, could you please explain what output of CD-HIT you used to generate HMMs?

Thank you for your attention!