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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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Protein Domain Search Query Returns Only One Hit Instead of Multiple Hits #182

Open yonatan212 opened 1 year ago

yonatan212 commented 1 year ago

I am attempting to perform a protein domain search using the following command:

easy-search ~/projects/predict_pae/data/ufl_str/human_ufl.pdb ddrgk_repit ~/Desktop/try.html tmp --format-mode 3 -e 10000001 --alt-ali 20 -c 0.02 --cov-mode 2 In the target "ddrgk_repit", there is only one wing_helix domain In the query: "ufl_str/human_ufl.pdb", there are protein include four wing_helix domains and half wing_helix domain. My goal is to find not just one hit but all possible hits and partial hits.

Any guidance or suggestions on how to modify the command or adjust parameters to achieve this would be greatly appreciated.

milot-mirdita commented 1 year ago

Can you try if it works correctly without the coverage parameters?

martin-steinegger commented 1 year ago

@yonatan212 our --alt-ali option functions by searching the query against the target to find the best local alignment. It then masks the identified parts in the target and searches again to find any new domains. This process repeats until no new domains are found. In order to work with your use-case you need to swap query and target.