search

steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
695 stars 92 forks source link

Questions on effects and usage of --num-iterations options #215

Closed yakomaxa closed 6 months ago

yakomaxa commented 7 months ago

We found that foldseek has option --num-iterations in a release note: https://github.com/steineggerlab/foldseek/releases/tag/4-645b789.

I'm interested in this but found no documentations on this.

What effect does this option have? I guess this is probably based on profile search and related to 3Di-based searches, but is this correct guess? Is this also applicable to searches based on TM-align?

Best regards

milot-mirdita commented 6 months ago

It does a PSI blast like search, from the initial sequence/structure to sequence/structure search, it generates a PSSM for each query then does profile to sequence/structure searches in multiple iterations.

We haven't extensively benchmarked this yet. We will do this at some point for some upcoming publication. But it should increase search sensitivity further.

yakomaxa commented 6 months ago

Thank you for clarification! I tried the option and it seems working correctly. I'm looking forward to seeing your publication on this.