Browsing MGnify IDs and clusters
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14 months ago
biomarco ▴ 50

I'm trying to familiarize with the MGnify database (https://www.ebi.ac.uk/metagenomics/) since I believe it would be a valuable resource for my research.

I'm encountering some difficulties with how to use it and would very much appreciate some help from you guys.

Basically I have 2 problems: 1) When I search a protein sequence into their clustered database (Sequence search button) I get to a page with many results. What's the reason why if I directly search for one of those accession ids using the search box on the homepage it doesn't find anything? (e.g. MGYP000524092069 won't work)

2) Since the search results are cluster representatives, how do I get to the whole cluster items?

metagenomics mgnify ebi • 676 views
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Entering edit mode
14 months ago
biomarco ▴ 50

I follow up with the solutions I found.

Question 1) To retrieve the sequences from accassion ids it seems not possible to use the MGnify website. Just look them up in the ESM Atlas as follows: https://api.esmatlas.com/fetchSequence/MGYP000611865938 It is also documented here: https://esmatlas.com/about

Question 2) To know the cluster items you have to look for the representatives in the file mgy_cluster_seqs.tsv.gz from http://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/current_release/

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