Searching against all the databases and specific organism

steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

https://foldseek.com

GNU General Public License v3.0

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Searching against all the databases and specific organism #251

Closed ahof1704 closed 3 months ago

ahof1704 commented 3 months ago

Hi,

Fantastic work! I have two questions: 1) Can I pass a list of databases I would like to search over? All the examples I have seen so far specify a single database, but I would like to search all the available databases, similar to what is done on the web application.

2) Can I specify the organism? I have a particular interest in human homologs.

Thanks!

milot-mirdita commented 3 months ago

1) No, you have to repeatedly call search/easy-search on each database. 2) --taxon-list 9606 is the parameter you are looking for.

ahof1704 commented 3 months ago

Thank you!